SecProbe.io

<DOCUMENT>
<TYPE>TEXT-EXTRACT
<SEQUENCE>2
<FILENAME>filename2.txt
<TEXT>
 June 17, 2025

Gisele Dion
Chief Accounting Officer
Alnylam Pharmaceuticals, Inc.
675 West Kendall Street
Henri A. Termeer Square
Cambridge, MA 02142

 Re: Alnylam Pharmaceuticals, Inc.
 Form 10-K for the fiscal year ended December 31, 2024
 Filed February 13, 2025
 File No. 001-36407
Dear Gisele Dion:

 We have completed our review of your filing. We remind you that the
company and
its management are responsible for the accuracy and adequacy of their
disclosures,
notwithstanding any review, comments, action or absence of action by the staff.

 Sincerely,

 Division of Corporation
Finance
 Office of Life Sciences
</TEXT>
</DOCUMENT>

CORRESP
 1
 filename1.htm

 Document Confidential Treatment Requested by Alnylam Pharmaceuticals, Inc. Pursuant to 17 C.F.R. Section 200.83 FOIA Confidential Treatment Request The entity requesting confidential treatment is: Alnylam Pharmaceuticals, Inc. 675 West Kendall Street, Henri A. Termeer Square Cambridge, MA 02142 Attention: Jeffrey V. Poulton May 22, 2025 VIA EDGAR AND ELECTRONIC MAIL Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attention: Frank Wyman; Daniel Gordon Re:    Alnylam Pharmaceuticals, Inc. Form 10-K for the Year Ended December 31, 2024 Filed February 13, 2025 File No. 001-36407 Dear Mr. Wyman and Mr. Gordon, On behalf of Alnylam Pharmaceuticals, Inc. (the “Company”), I am submitting this letter in response to comments from the staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) received by letter dated May 9, 2025, concerning the Company’s Form 10-K for the year ended December 31, 2024 (the "Form 10-K"), filed with the Commission on February 13, 2025. To assist your review, the text of the Staff’s comments is presented in italics below. Form 10-K for the fiscal year ended December 31, 2024 Notes to Consolidated Financial Statements 4. Net Revenues from Collaborations Regeneron Pharmaceuticals, Inc., page 105 675 West Kendall Street – Henri A. Termeer Square ● Cambridge MA, 02142 main 617.551.8200 ● fax 617.551.8101 ● www.alnylam.com - 2 - May 22, 2025 1. Please link revenue recognized under the Regeneron collaboration and associated deferred revenue on page 108 to corresponding amounts reported in the financial statements for each period presented. Revise your disclosure accordingly. Response Revenue recognized under the Regeneron collaboration is presented in net revenues from collaborations in the consolidated statements of operations and comprehensive loss and the associated deferred revenue is presented within deferred revenue and deferred revenue, net of current portion in the consolidated balance sheets. The composition of net revenues from collaborations in the consolidated statements of operations and comprehensive loss, as disclosed in Note 4 of the Form 10-K (page 102), is as follows: (in thousands) Years ended December 31, 2024 2023 2022 Roche $ 119,489 $ 337,802 $ — Regeneron Pharmaceuticals 302,798 100,468 87,844 Novartis AG 79,759 86,727 43,159 Other 8,175 21,188 3,909 Total net revenues from collaborations $ 510,221 $ 546,185 $ 134,912 In addition, also in Note 4 the Company disclosed additional detail on revenue recognized from the Regeneron collaboration as follows: (in thousands) Years ended December 31, 2024 2023 2022 Research Services Obligation (as presented on page 108) $ 39,097 $ 80,200 $ 28,600 C5 License Obligation (as presented on page 108) 38,341 (15,100) 32,500 C5 Monotherapy Obligation (as discussed on page 107) 191,520 — — C5 Co-Co Obligation (recognized prior to June 2024 Amendment) 1 700 7,400 20,080 Other license programs 2 33,140 27,968 6,664 Total $ 302,798 $ 100,468 $ 87,844 1 Revenue recognized for the C5 Co-Co Obligation is not separately disclosed because the disclosure on page 108 provides a summary of revenue recognized during the period for the remaining unsatisfied performance obligations as of the balance sheet date in accordance with ASC 606-10-50-8. In June 2024, the C5 Co-Co Collaboration Agreement was terminated. Therefore, the Company's obligation under the C5 Co-Co performance obligation ended prior to and is no longer unsatisfied as of December 31, 2024. 2 Revenue recognized for the “ Other license programs ” relates to seven separate programs subject to individual license agreements with Regeneron that are not material for separate disclosure. 675 West Kendall Street – Henri A. Termeer Square ● Cambridge MA, 02142 main 617.551.8200 ● fax 617.551.8101 ● www.alnylam.com - 3 - May 22, 2025 The composition of deferred revenue and deferred revenue, net of current portion as presented in the consolidated balance sheet as of December 31, 2024 is as follows: (in thousands) Current Non-current Total Research Services Obligation $ 41,155 $ — $ 41,155 C5 License Obligation 12,018 — 12,018 Regeneron Technology Transfer Obligation 2,307 — 2,307 Rounding difference 1 — 1 Total $ 55,481 $ — $ 55,481 The composition of deferred revenue and deferred revenue, net of current portion as presented in the consolidated balance sheet as of December 31, 2023 is as follows: (in thousands) Current Non-current Total Research Services Obligation $ 61,500 $ 1,900 $ 63,400 C5 License Obligation 27,500 — 27,500 C5 Co-Co Obligation — 186,200 186,200 Other deferred revenue 3 13,663 — 13,663 Total 4 $ 102,663 $ 188,100 $ 290,763 3 “Other deferred revenue” does not relate to our arrangements with Regeneron. This amount represents our obligation to deliver products and/or provide services to other parties. 4 The difference between the "Total" amounts in the table above and the consolidated balance sheet is related to deferred product revenues. Two of the Company's remaining performance obligations as of December 31, 2024 (that is, the C5 License Obligation and Regeneron Technology Transfer Obligation) were completed in the first quarter of 2025. The Company will enhance its disclosure in future filings, starting with the Form 10-Q for the three- and six-month periods ending June 30, 2025, as it relates to revenue recognized from the Company's arrangements with Regeneron. The disclosure will also include a statement that revenue earned from these arrangements is presented in net revenues from collaborations in the consolidated statements of operations and comprehensive loss and the remaining deferred revenue is presented within deferred revenue in the consolidated balance sheets. To enhance its disclosures in future Form 10-K filings, the Company plans to replace the tables that were included in its Form 10-K with the tables presented in Appendix A. The Company also plans to include similar tables to supplement the disclosures in its Form 10-Q filings, beginning with its Form 10-Q for the three- and six-month periods ending June 30, 2025. In addition, provide the following information related to your accounting treatment for the June 2024 Amendment. • Explain why the transaction price allocated to the new C5 Monotherapy Obligation was recognized at a point in time, while the transaction price allocated to the legacy C5 License Obligation is recognized over time, given your apparent continuing obligations to support these two licenses. 675 West Kendall Street – Henri A. Termeer Square ● Cambridge MA, 02142 main 617.551.8200 ● fax 617.551.8101 ● www.alnylam.com - 4 - May 22, 2025 Response Legacy C5 License Obligation The legacy C5 License Agreement from 2019 previously provided Regeneron with rights to the Company's cemdisiran product candidate solely to be used in combination with pozelimab, Regeneron’s drug candidate. Regeneron is responsible for the development and commercialization of cemdisiran to be used in combination with pozelimab. The Company's obligations included granting Regeneron a worldwide license to cemdisiran for combination therapies, manufacturing and supply and development services. When the Company entered into the C5 License Agreement in 2019, it concluded, in accordance with ASC 606-10-25-19, that the worldwide license to cemdisiran for combination therapeutics is not capable of being distinct nor distinct within the context of the contract as Regeneron could not benefit from the license on its own or with other readily available resources. At the time this arrangement was executed, RNAi technology was a new technology and contract development and manufacturing organizations did not have the technical expertise and know-how to support the manufacturing process related to RNAi technology. Given the early-stage nature of the intellectual property, and highly specialized and new nature of RNAi technology, no one other than the Company could perform the manufacturing and supply services. The Company also expected that the development services performed by it would involve significant modification to the intellectual property. Therefore, the Company concluded that the license was not distinct from the manufacturing and supply services or the development services. The Company combined the license to cemdisiran for combination therapies, as well as the manufacturing and supply and development services obligations into one performance obligation which the Company refers to as the C5 License Obligation. The Company measures proportional performance for the C5 License Obligation over time using an input method based on cost incurred relative to the total expected costs to be incurred to determine the proportion of effort incurred as a percentage of the total effort the Company expects to expend. This ratio is applied to the transaction price for the C5 License Obligation to determine the amount of revenue to recognize. Pursuant to ASC 606-10-25-35, as circumstances change over time, the Company updates its measure of progress to reflect any changes in the outcome of the performance obligation. The June 2024 Amendment did not change the Company's legacy C5 License Obligation. The Company's C5 License Obligation was partially satisfied at the time of the contract modification, and the Company remained obligated to provide manufacturing and supply and development services for cemdisiran as a combination therapy to Regeneron. As the Company's C5 License Obligation was only partially satisfied at the time of the contract modification, the Company continues to recognize revenue over time using the input-based method described above. The Company recorded a cumulative catch-up at the time of the contract modification, which is discussed below in more detail. C5 Monotherapy Obligation In 2024, the C5 Co-Co Collaboration Agreement related to cemdisiran as a monotherapy was terminated, and at the same time the Company granted Regeneron a worldwide license to cemdisiran as a monotherapy. Regeneron is now fully responsible for the development, manufacturing and commercialization of cemdisiran as a monotherapy. By granting Regeneron a worldwide license to cemdisiran as a monotherapy, the Company transferred new rights to the cemdisiran monotherapy intellectual property to Regeneron. The Company no longer had any future obligations to perform development, manufacturing and commercialization activities for cemdisiran as a monotherapy. 675 West Kendall Street – Henri A. Termeer Square ● Cambridge MA, 02142 main 617.551.8200 ● fax 617.551.8101 ● www.alnylam.com - 5 - May 22, 2025 The Company concluded, in accordance with ASC 606-10-25-19, that the license to develop, manufacture and commercialize cemdisiran as a monotherapy is a distinct good. As a global, mature, fully integrated biopharmaceutical company, Regeneron has the ability on its own or with the use of readily available resources to generate economic benefit from the license. The manufacturing process to produce cemdisiran is no longer unique, specialized or requires the Company’s expertise and knowledge in order to benefit from the license, as it did in 2019. Over the last five years, there has been substantial advancement in RNAi technologies, including the commercialization of multiple products to treat disease using RNAi technology and a significant number of companies using this technology to identify new medicines. Additionally, contract development and manufacturing organizations have gained technical expertise and know-how to support the manufacturing process related to RNAi technology. At the transfer of control of the license in June 2024, Regeneron has the knowledge and expertise as well as the development, manufacturing and commercial processes in place to generate economic benefit from the license. Regeneron can begin to use and benefit from the license at this time and Regeneron also has the right to sublicense the intellectual property, which gives the license standalone value for which Regeneron can benefit from the license on its own. Therefore, the transaction price of $191.5 million allocated to the C5 Monotherapy Obligation was recognized immediately as this obligation was satisfied at a point in time upon transfer of the license to Regeneron. • Describe and quantify key assumptions underlying your determination of standalone selling price of $322,000 [sic] for the C5 Monotherapy Obligation, including discount rates, forecasted earnings, duration of the commercial period and adjustments for probability of success. Response The Company developed the estimated standalone selling price of $332,000 for the cemdisiran monotherapy license granted under the C5 Monotherapy Obligation using the adjusted market assessment approach based on a discounted cash flow model that establishes the forecasted earnings during the commercial period for cemdisiran as a monotherapy adjusted for probability of success. The key assumptions underlying our determination of the standalone selling price are (all dollar amounts below are presented in thousands): • Revenue – The Company's discounted cash flow model starts in [***] a nd continues until [***] . The last cemdisiran monotherapy patent expires in [***] . The substantial majority of the revenue from cemdisiran as a monotherapy is estimated to occur between [***] . The Company believes that cemdisiran as a monotherapy will continue to [***] . The range of annual revenue is [***] until [***] , to a peak of [***] . • Probability of Success - The Company incorporated a cumulative phase of outcome probability of success of [***], consistent with our and industry established standards, given the current stage of development for cemdisiran as a monotherapy. At the time of the contract modification, cemdisiran was in the second phase of clinical development. The Company considered a [***] likelihood of a successful outcome of cemdisiran in the third phase of clinical development and a [***] likelihood of cemdisiran receiving regulatory approval if the second and third phase of the clinical development process are successful. In other words, the [***] probability of success represents [***] of the [***] chance of a successful outcome of cemdisiran in the third phase of clinical development. • Research and Development Expense – The Company estimated research and development expenses based on the expected costs to be incurred to complete the clinical development process and any open label expansion trials for cemdisiran as a monotherapy. • Other Operating Expenses – Other operating expenses primarily represent commercial expenses and general and administrative expenses. The Company estimated these expenses as a consistent percentage of revenue based on our historical experience with other commercial products. 675 West Kendall Street – Henri A. Termeer Square ● Cambridge MA, 02142 main 617.551.8200 ● fax 617.551.8101 ● www.alnylam.com - 6 - May 22, 2025 • Discount rate – The Company utilized a discount rate of [***] which was determined based on an estimated market participant weighted average cost of capital. • Explain how you determined revenue recognized in 2024 for the Research Services Obligation and C5 License Obligation, particularly expected performance periods, and why no revenue was recognized for the Regeneron Technology Transfer Obligation. Response For the Research Services Obligation and the legacy C5 License Obligation the Company measured proportional performance over time using an input-based method based on costs incurred (the numerator in the cost-to-cost model) relative to the total expected costs to be incurred (the denominator in the cost-to-cost model) to determine the proportion of effort incurred as a percentage of total effort the Company expects to expend. This ratio is applied to the transaction price allocated to each obligation to determine the

<DOCUMENT>
<TYPE>TEXT-EXTRACT
<SEQUENCE>2
<FILENAME>filename2.txt
<TEXT>
 May 9, 2025

Gisele Dion
Chief Accounting Officer
Alnylam Pharmaceuticals, Inc.
675 West Kendall Street
Henri A. Termeer Square
Cambridge, MA 02142

 Re: Alnylam Pharmaceuticals, Inc.
 Form 10-K for the fiscal year ended December 31, 2024
 Filed February 13, 2025
 File No. 001-36407
Dear Gisele Dion:

 We have limited our review of your filing to the financial statements
and related
disclosures and have the following comment.

 Please respond to this letter within ten business days by providing the
requested
information or advise us as soon as possible when you will respond. If you do
not believe a
comment applies to your facts and circumstances, please tell us why in your
response.

 After reviewing your response to this letter, we may have additional
comments.

Form 10-K for the fiscal year ended December 31, 2024
Notes to Consolidated Financial Statements
4. Net Revenues from Collaborations
Regeneron Pharmaceuticals, Inc., page 105

1. Please link revenue recognized under the Regeneron collaboration and
associated
 deferred revenue on page 108 to corresponding amounts reported in the
financial
 statements for each period presented. Revise your disclosure
accordingly. In addition,
 provide the following information related to your accounting treatment
for the June
 2024 Amendment.
 Explain why the transaction price allocated to the new C5
Monotherapy
 Obligation was recognized at a point in time, while the transaction
price allocated
 to the legacy C5 License Obligation is recognized over time, given
your apparent
 continuing obligations to support these two licenses.
 Describe and quantify key assumptions underlying your determination
of
 May 9, 2025
Page 2

 standalone selling price of $322,000 for the C5 Monotherapy
Obligation,
 including discount rates, forecasted earnings, duration of the
commercial
 period and adjustments for probability of success.
 Explain how you determined revenue recognized in 2024 for the
Research
 Services Obligation and C5 License Obligation, particularly expected
 performance periods, and why no revenue was recognized for the
Regeneron
 Technology Transfer Obligation.
 Demonstrate that the cumulative catch up adjustment for the
remaining Research
 Services Obligation and C5 License Obligation was not significant.

 In closing, we remind you that the company and its management are
responsible for
the accuracy and adequacy of their disclosures, notwithstanding any review,
comments,
action or absence of action by the staff.

 Please contact Frank Wyman at 202-551-3660 or Daniel Gordon at
202-551-3486
with any questions.

 Sincerely,

 Division of
Corporation Finance
 Office of Life
Sciences
</TEXT>
</DOCUMENT>

September 25, 2024
Jeffrey Poulton
Chief Financial Officer
Alnylam Pharmaceuticals, Inc.
675 West Kendall Street
Henri A. Termeer Square
Cambridge, MA 20142
Re:Alnylam Pharmaceuticals, Inc.
Form 10-K for the Fiscal Year Ended December 31, 2023
Filed February 15, 2024
File No. 001-36407
Dear Jeffrey Poulton:
            We have completed our review of your filing. We remind you that the company and its
management are responsible for the accuracy and adequacy of their disclosures, notwithstanding
any review, comments, action or absence of action by the staff.
Sincerely,
Division of Corporation Finance
Office of Life Sciences

CORRESP
1
filename1.htm

Document

August 22, 2024

VIA EDGAR

United States Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, D.C. 20549

Attention: Frank Wyman, Angela Connell

Re:    Alnylam Pharmaceuticals, Inc.

Form 10-K for the Year Ended December 31, 2023

Filed February 15, 2024

File No. 001-36407

Dear Mr. Wyman and Ms. Connell:

On behalf of Alnylam Pharmaceuticals, Inc. (the “Company,” “we,” or “our”), I am submitting this letter in response to comments from the staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) received by letter dated August 12, 2024, concerning the Company’s Form 10-K for the year ended December 31, 2023, filed with the Commission on February 15, 2024.

To assist your review, the text of the Staff’s comments is presented in italics below.

Form 10-K for the Year Ended December 31, 2023

Notes to Consolidated Financial Statements

4. Net Revenues from Collaborations, page 107

1.We note your tabular disclosure at the bottom of page 107 that quantifies the research and development (R&D) expenses incurred by collaborator and type that are directly attributable to your collaboration agreements. Please explain to us how this disclosure relates to your net revenues from collaborations. Using the Roche collaboration as an example, your disclosure on page 110 indicates that you recognized collaboration revenue of $24 million during 2023 related to your Development Services Obligation. Please

675 West Kendall Street – Henri A. Termeer Square  ●  Cambridge MA, 02142
main 617.551.8200  ●  fax 617.551.8101 ● www.alnylam.com

 2

 August 22, 2024

explain how this amount relates to the $44.6 million in total R&D expenses attributed to the Roche collaboration as disclosed on page 107. In addition, to the extent applicable, please explain how the $547 million additional variable consideration attributed to cost reimbursement from development and manufacturing services and technology transfer related to the Roche Performance Obligations was calculated.

Response to Comment #1:

The table at the bottom of page 107 discloses the type and amount of research and development (“R&D”) expenses incurred for the Company's collaborations. Each of our collaboration agreements has unique performance obligations and cost sharing mechanisms. For our collaboration with Regeneron Pharmaceuticals, Inc. (“Regeneron”), revenue is recognized on a cost-to-cost input method and the costs used to measure both costs incurred and total costs are only those that relate to these performance obligations. Under the Company’s Collaboration and License Agreement with F. Hoffmann-La Roche Ltd. and Genentech, Inc. (together, “Roche”), dated as of July 21, 2023 (the “Roche Agreement”), we are reimbursed based on a percentage of the cost related to the R&D performance obligation. As requested by the Staff, we explain this in more detail below using our collaboration with Roche as an example.

Roche

Under the Roche Agreement, the Company has a performance obligation under Accounting Standards Codification (“ASC”) 606 and is obligated to perform development services, including the manufacture of clinical supply to support the regulatory approval of zilebesiran (the “Roche Development Services Obligation”). The Company is responsible for 40% and Roche is responsible for 60% of the costs incurred to perform the Roche Development Services Obligation.

At inception of the Roche Agreement, based on the development plan agreed to by the Company and Roche (the “Development Plan”), the Company was able to estimate the development activities it will perform under the Roche Development Services Obligation and the reimbursement that it is entitled to receive from Roche. The Company used the expected value method and estimated the expected value amount as $545 million. The estimated expected value amount represents 60% of the total cost (the Roche share) per the Development Plan based on the hours and costs expected to be incurred to perform all of the development activities until commercialization, risk adjusted based on the probability of successful completion of all of the phases which are contingent upon future regulatory events. The Company concluded it is probable that a significant reversal of cumulative revenue will not occur in the future if some amount of the variable payments are not ultimately paid, because the cost reimbursement amounts are only recognized as revenue as the Company performs the development activities under the Roche Development Services Obligation.

During the year ended December 31, 2023, the Company incurred $45 million in R&D expenses related to the Roche collaboration and recognized collaboration revenue of $24 million related to

675 West Kendall Street – Henri A. Termeer Square  ● Cambridge MA, 02142
main 617.551.8200  ●  fax 617.551.8101 ●  www.alnylam.com

 3

 August 22, 2024

the Roche Development Services Obligation. Of the $45 million in R&D expenses incurred, approximately $40 million related to the Roche Development Services Obligation.

The Company recognizes the consideration associated with the Roche Development Services Obligation using the cost-to-cost method which is based on cost incurred (the numerator in the cost-to-cost model) relative to the total estimated cost of the obligation (the denominator in the cost-to-cost-model) to determine the proportion of effort incurred as a percentage of total effort the Company expects to expend. This ratio is applied to the transaction price allocated to the obligation. As of December 31, 2023, the Company is approximately 4% complete with the Roche Development Services Obligation and has recognized $24 million of the $545 million transaction price associated with this obligation.

As all costs in the cost-to-cost model are allowable for reimbursement from Roche, and the assumptions used to determine the total estimated cost of the obligation (denominator in the cost-to-cost model) are consistent with the assumptions used to determine the transaction price associated with the obligation, the collaboration revenue recognized will approximate 60% of the actual reimbursable costs incurred.

Therefore, $24 million of collaboration revenue recognized under the cost-to-cost model can also be calculated as the $40 million of R&D expenses related to the Roche Development Services, multiplied by 60%, which is the Company’s reimbursement amount from Roche.

The Company also has an obligation to perform a technology transfer of the existing manufacturing process for zilebesiran (the “Roche Technology Transfer Obligation”). The Company used the expected value method to estimate the expected value amount of $2 million based on the estimated costs expected to be incurred to perform the technology transfer activities. The Company did not recognize any collaboration revenue for the Roche Technology Transfer Obligation in the year ended December 31, 2023.

Regeneron

The Company recognizes revenue related to its collaboration with Regeneron over time using an input-based method on costs incurred relative to the total expected costs to be incurred for each of the identified performance obligations (“percentage of completion”).  The specific amount of collaboration revenue for the period is determined by applying the percentage of completion to the transaction price allocated to each performance obligation.  Hence, the R&D costs disclosed in the table on page 107 determine the extent of progress toward completion of the R&D services, but our collaboration revenue is based on the consideration allocated to the performance obligation.

2.Please explain the circumstances that resulted in a reversal of revenue in the amount of $15.5 million related to your Regeneron C5 License Obligation during 2023 as disclosed on page 113.

675 West Kendall Street – Henri A. Termeer Square  ● Cambridge MA, 02142
main 617.551.8200  ●  fax 617.551.8101 ●  www.alnylam.com

 4

 August 22, 2024

Response to Comment #2:

During 2019, the Company entered into a global, strategic collaboration with Regeneron to discover, develop and commercialize RNAi therapeutics for a broad range of diseases. At the inception of the Regeneron collaboration, the Company identified an obligation to provide Regeneron with a worldwide license to cemdisiran for combination therapies, manufacturing and supply and development service obligations (the “C5 License Obligation”). The Company determined that the worldwide license to cemdisiran for combination therapies is not distinct from the manufacturing and supply and development service obligations as Regeneron cannot benefit on its own from the value of the license without receipt of the supply. Therefore, the C5 License Obligation is a single performance obligation.

The C5 License Obligation is satisfied over time using an input-based method based on costs incurred relative to the total expected costs to be incurred.  The amount of revenue recognized during each period for the C5 License Obligation is impacted by changes in the percent complete for the period, which is driven by changes in either costs incurred to date (the numerator in the percentage calculation) or changes in total expected costs to be incurred (the denominator in the percentage calculation).  Pursuant to ASC 606-10-25-35, as circumstances change over time, the Company updates its measure of progress to reflect any changes in the outcome of the performance obligation. Such changes to the Company’s measure of progress are accounted for as a change in accounting estimate.

During the fourth quarter of 2023, Regeneron increased the scope of the manufacturing and supply activities for the C5 License Obligation to support the potential future manufacturing of cemdisiran as a commercial drug. The Company assessed the facts and circumstances surrounding this change, which resulted from new information communicated by Regeneron, and determined that such change represents a change in estimate in the fourth quarter of 2023.

The total expected costs to be incurred to perform the C5 License Obligation increased in the fourth quarter of 2023 to reflect the additional hours and costs expected to be incurred by the Company to perform the manufacturing and supply activities.  When completing the Company's periodic update to its estimated costs to complete and, in turn, the cumulative progress toward completion of the C5 License Obligation, the Company used its updated estimate of total expected costs to be incurred as the denominator in the cost-to-cost model and recalculated the cumulative amount of revenue that should be recognized. That cumulative amount of revenue is compared to the cumulative amount of revenue recognized as of the prior period end (December 31, 2022). As indicated in the table below, as the estimate of total expected costs to be incurred in the denominator increased, the percentage of completion and the cumulative amount of revenue recognized decreased, resulting in the reversal of revenue in the amount of $15.1 million.

675 West Kendall Street – Henri A. Termeer Square  ● Cambridge MA, 02142
main 617.551.8200  ●  fax 617.551.8101 ●  www.alnylam.com

 5

 August 22, 2024

(In thousands, except percentages)  December 31, 2022  December 31, 2023  Reversal of revenue during the year ended December 31, 2023

Inception-to-date costs incurred  $27,178  $32,415

Expected costs to be incurred

  $31,392  $58,270

Percentage of completion  87  %  56  %

Transaction price

  $97,185  $124,106

Inception-to-date revenue recognized  $84,139  $69,039  $(15,100)

*      *     *     *     *

675 West Kendall Street – Henri A. Termeer Square  ● Cambridge MA, 02142
main 617.551.8200  ●  fax 617.551.8101 ●  www.alnylam.com

 6

 August 22, 2024

Please do not hesitate to email me at jpoulton@alnylam.com or Gisele Dion, the Company's Chief Accounting Officer, at gdion@alnylam.com with any questions or further comments you may have regarding this filing or if you wish to discuss the above responses.

 Sincerely,

 /s/ Jeffrey V. Poulton

 Jeffrey V. Poulton
Executive Vice President, Chief Financial Officer

675 West Kendall Street – Henri A. Termeer Square  ● Cambridge MA, 02142
main 617.551.8200  ●  fax 617.551.8101 ●  www.alnylam.com

August 12, 2024
Jeffrey Poulton
Chief Financial Officer
Alnylam Pharmaceuticals, Inc.
675 West Kendall Street
Henri A. Termeer Square
Cambridge, MA 20142
Re:Alnylam Pharmaceuticals, Inc.
Form 10-K for the Fiscal Year Ended December 31, 2023
Filed February 15, 2024
File No. 001-36407
Dear Jeffrey Poulton:
            We have limited our review of your filing to the financial statements and related
disclosures and have the following comments.
            Please respond to this letter within ten business days by providing the requested
information or advise us as soon as possible when you will respond. If you do not believe a
comment applies to your facts and circumstances, please tell us why in your response.
            After reviewing your response to this letter, we may have additional comments.
Form 10-K for the Fiscal Year Ended December 31, 2023
Notes to Consolidated Financial Statements
4. Net Revenues from Collaborations, page 107
1.We note your tabular disclosure at the bottom of page 107 that quantifies the research and
development (R&D) expenses incurred by collaborator and type that are directly
attributable to your collaboration agreements.  Please explain to us how this disclosure
relates to your net revenues from collaborations.  Using the Roche collaboration as an
example, your disclosure on page 110 indicates that you recognized collaboration revenue
of $24 million during 2023 related to your Development Services Obligation. Please
explain how this amount relates to the $44.6 million in total R&D expenses attributed to
the Roche collaboration as disclosed on page 107.  In addition, to the extent applicable,
please explain how the $547 million additional variable consideration attributed to cost
reimbursement from development and manufacturing services and technology transfer
related to the Roche Performance Obligations was calculated.

August 12, 2024
Page 2
2.Please explain the circumstances that resulted in a reversal of revenue in the amount of
$15.5 million related to your Regeneron C5 License Obligation during 2023 as disclosed
on page 113.
            In closing, we remind you that the company and its management are responsible for the
accuracy and adequacy of their disclosures, notwithstanding any review, comments, action or
absence of action by the staff.
            Please contact Frank Wyman at 202-551-3660 or Angela Connell at 202-551-3426 with
any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences

March 20, 2019
John M. Maraganore, Ph.D.
Chief Executive Officer
Alnylam Pharmaceuticals, Inc.
300 Third Street
Cambridge, MA 02142
Re:Alnylam Pharmaceuticals, Inc.
Preliminary Proxy Statement on Schedule 14A
Filed March 11, 2019
File No. 001-36407
Dear Dr. Maraganore:
            We have completed our review of your filing.  We remind you that the company and its
management are responsible for the accuracy and adequacy of their disclosures, notwithstanding
any review, comments, action or absence of action by the staff.
Sincerely,
Division of Corporation Finance
Office of Healthcare & Insurance
cc:       Gregg L. Katz, Esq.

January 23, 2018
Michael P. Mason
Vice President of Finance and Treasurer
Alnylam Pharmaceuticals, Inc.
300 Third Street
Cambridge, MA 02142
ALNYLAM PHARMACEUTICALS, INC.
Form 10-K for the Fiscal Year Ended December 31, 2016
Filed February 15, 2017
File No. 001-36407Re:
Dear Mr. Mason:
            We have completed our review of your filing. We remind you that the company and its
management are responsible for the accuracy and adequacy of their disclosures, notwithstanding
any review, comments, action or absence by the staff.
Division of Corporation Finance
Office of Healthcare & Insurance

CORRESP
1
filename1.htm

CORRESP

 Alnylam Pharmaceuticals, Inc.

300 Third Street

 Cambridge, MA
02142

 January 19, 2018

 United States
Securities and Exchange Commission

 Division of Corporation Finance

100 F Street N.E.

 Washington, D.C. 20549

Attention: Frank Wyman and Jim Rosenberg, Office of Healthcare & Insurance

 RE:

Alnylam Pharmaceuticals, Inc.

Form 10-K for Fiscal Year Ended December 31, 2016

Filed February 15, 2017

File No. 001-36407

 Dear Messrs. Wyman and Rosenberg:

This letter is being furnished in response to the comments of the staff (the “Staff”) of the Securities and Exchange Commission (the
“Commission”) in the Commission’s letter dated January 8, 2018 (the “Comment Letter”) to Michael P. Mason, Vice President of Finance and Treasurer of Alnylam Pharmaceuticals, Inc. (the “Company”), with respect
to the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2016, and the documents incorporated by reference therein. The responses set forth below have been organized in the
same manner in which the Commission’s comments and headings were organized in the Comment Letter.

 Comment: Notes to the Consolidated Financial
Statements – 3. Significant Agreements, page 97

 We acknowledge the information provided in your response to our prior comment 1 of our
November 27, 2017 comment letter. As required by ASC 730-20-50-1b, please confirm to us that you will disclose herein the
costs incurred for each of your significant agreements. We would expect the amount disclosed to include the costs you provided in your response and your reasonable estimate of other costs incurred albeit for which you may not track separately for
each agreement. In this regard, it would appear that a reasonable estimate would be attainable, given that you track hours incurred for the purpose of billing your counterparties. Finally, we believe additional disclosure in your research and
development expense discussion of your MD&A of the nature and amount of research and development costs incurred related to your agreements would be informative.

Response

 In future periodic filings, including the Form 10-K for the fiscal year ended December 31, 2017, the Company will revise its disclosure to disclose the costs incurred for each of the Company’s significant agreements, including the costs provided in the
Company’s response letter dated December 11, 2017, and a reasonable estimate of other costs incurred, and the Company will include additional disclosure in the research and development expense discussion of MD&A of the nature and
amount of research and development costs incurred related to its significant agreements.

 Messrs. Frank Wyman and Jim Rosenberg

U.S. Securities and Exchange Commission

 January 19, 2018

 Page 2

 If you have any questions with regard to the Company’s responses or would like to
discuss any of the matters covered in this letter, please contact the undersigned at (617) 551-8200 or Gregg L. Katz of Goodwin Procter LLP, the Company’s outside counsel, at (617) 570-1000.

Sincerely,

/s/ Michael P. Mason

Michael P. Mason

Vice President, Finance and Treasurer

January 8, 2018
Michael P. Mason
Vice President of Finance and Treasurer
Alnylam Pharmaceuticals, Inc.
300 Third Street
Cambridge, MA 02142
Re:ALNYLAM PHARMACEUTICALS, INC.
Form 10-K for Fiscal Year Ended December 31, 2016
Filed February 15, 2017
File No. 001-36407
Dear Mr. Mason:
            We have reviewed your December 11, 2017 response to our comment letter and have the
following comment. In our comment, we may ask you to provide us with information so we may
better understand your disclosure.
            Please respond to the comment within ten business days by providing the requested
information or advise us as soon as possible when you will respond. If you do not believe our
comment applies to your facts and circumstances, please tell us why in your response.
            After reviewing your response to the comment, we may have additional comments.
Notes to Consolidated Financial Statements
3. Significant Agreements, page 97
1.We acknowledge the information provided in your response to our prior comment 1 of
our November 27, 2017 comment letter. As required by ASC 730-20-50-1b, please
confirm to us that you will disclose herein the costs incurred for each of your significant
agreements. We would expect the amount disclosed to include the costs you provided in
your response and your reasonable estimate of other costs incurred albeit for which you
may not track separately for each agreement. In this regard, it would appear that a
reasonable estimate would be attainable, given that you track hours incurred for the
purpose of billing your counterparties. Finally, we believe additional disclosure in your
research and development expense discussion of your MD&A of the nature and amount
of research and development costs incurred related to your agreements would be

 FirstName LastNameMichael P. Mason
 Comapany NameAlnylam Pharmaceuticals, Inc.
 June 16, 2017 Page 2
 FirstName LastName
Michael P. Mason
Alnylam Pharmaceuticals, Inc.
January 8, 2018
Page 2
informative.
            You may contact Frank Wyman at 202-551-3660  or Jim Rosenberg at 202-551-3679
with any questions.
Division of Corporation Finance
Office of Healthcare & Insurance

CORRESP
1
filename1.htm

CORRESP

 Alnylam Pharmaceuticals, Inc.

300 Third Street

 Cambridge, MA
02142

 December 11, 2017

 United States
Securities and Exchange Commission

 Division of Corporation Finance

100 F Street N.E.

 Washington, D.C. 20549

Attention: Frank Wyman and Jim Rosenberg, Office of Healthcare & Insurance

RE:
Alnylam Pharmaceuticals, Inc.

 Form 10-K for Fiscal
Year Ended December 31, 2016

 Filed February 15, 2017

File No. 001-36407

Dear Messrs. Wyman and Rosenberg:

 This letter is being
furnished in response to the comments of the staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) in the Commission’s letter dated November 27, 2017 (the “Comment Letter”) to
Michael P. Mason, Vice President of Finance and Treasurer of Alnylam Pharmaceuticals, Inc. (the “Company”), with respect to the Company’s Annual Report on Form 10-K for the fiscal year
ended December 31, 2016, and the documents incorporated by reference therein. The responses set forth below have been organized in the same manner in which the Commission’s comments and headings were organized in the Comment Letter.

Comment: Notes to the Consolidated Financial Statements – 3. Significant Agreements, page 97

For each significant agreement, please provide us a schedule by type and amount of costs incurred included in research and development expenses for the
years ended December 31, 2015 and 2016 and for the nine months ended September 30, 2017. Also provide us a similar schedule for general and administrative expenses or confirm that you have not incurred material general and administrative
expenses related to your significant agreements.

 Messrs. Frank Wyman and Jim Rosenberg

U.S. Securities and Exchange Commission

 December 11, 2017

Page 2

 Response

The research and development costs incurred for each significant agreement during the periods referenced above primarily consist of costs incurred for external
development and manufacturing services for which the Company is reimbursed and licensing payments made to the licensor. As noted in Part II, Item 7, “Management’s Discussion and Analysis of Financial Condition and Results of
Operations,” a significant portion of the Company’s research and development costs, including overhead and compensation and related costs, are not tracked by project as they benefit multiple projects or the Company’s technology
platform. For the years ended December 31, 2015 and 2016 and the nine months ended September 30, 2017, the Company did not incur material general and administrative expenses related to its significant agreements.

The Company has provided to the Staff, under separate cover and on a confidential and supplemental basis pursuant to Rule
12b-4 under the Securities Exchange Act of 1934, as amended, additional information requested in the Staff’s comment. The Company also has requested confidential treatment of this information pursuant to
17 C.F.R. § 200.83.

 If you have any questions with regard to the Company’s responses or would like to discuss any of the matters covered in
this letter, please contact the undersigned at (617) 551-8200 or Gregg L. Katz of Goodwin Procter LLP, the Company’s outside counsel, at (617) 570-1000.

Sincerely,

 /s/ Michael P. Mason

Michael P. Mason

Vice President, Finance and Treasurer

November 27, 2017
Michael P. Mason
Vice President of Finance and Treasurer
Alnylam Pharmaceuticals, Inc.
300 Third Street
Cambridge, MA 02142
Re:ALNYLAM PHARMACEUTICALS, INC.
Form 10-K for the Fiscal Year Ended December 31, 2016
Filed February 15, 2017
File No. 001-36407
Dear Mr. Mason:
            We have limited our review of your filing to the financial statements and related
disclosures and have the following comment. In our comment, we may ask you to provide us
with information so we may better understand your disclosure.
            Please respond to the comment within ten business days by providing the requested
information or advise us as soon as possible when you will respond.  If you do not believe our
comment applies to your facts and circumstances, please tell us why in your response.
            After reviewing your response to the comment, we may have additional comments.
Form 10-K for the Year Ended December 31, 2016
Notes to Consolidated Financial Statements
3. Significant Agreements , page 97
1.For each significant agreement, please provide us a schedule by type and amount of costs
incurred included in research and development expenses for the years ended December
31, 2015 and 2016 and for the nine months ended September 30, 2017.  Also provide us a
similar schedule for general and administrative expenses or confirm that you have not
incurred material general and administrative expenses related to your significant
agreements.
            In closing, we remind you that the company and its management are responsible for the
accuracy and adequacy of their disclosures, notwithstanding any review, comments, action or

 FirstName LastNameMichael P. Mason
 Comapany NameAlnylam Pharmaceuticals, Inc.
 June 16, 2017 Page 2
 FirstName LastName
Michael P. Mason
Alnylam Pharmaceuticals, Inc.
November 27, 2017
Page 2
absence of action by the staff.
            You may contact Frank Wyman at 202-551-3660 or Jim Rosenberg at 202-551-3679
with any questions.
Division of Corporation Finance
Office of Healthcare & Insurance

Mail Stop 4720

December  23, 2015

VIA E -mail
John M. Maraganore, Ph. D.
Chief Executive Officer
Alnylam Pharmaceuticals, Inc.
300 Third Street ,
Cambridge, MA  02142

Re: Alnylam Pharmaceuticals, Inc.
 Form 10-K for Fiscal Year Ended December 31, 2014
Filed February 13 , 2015
File No. 001-36407

Dear Dr. Maraganore :

We have comple ted our review of your filing .  We remind you that our comments or
changes to disclosure in response to our comments do not foreclose the Commission from taking
any action with respect  to the company or the filing  and the company may not assert staff comments
as a defense in any proceeding initiated by the Commission or any person under the federal
securi ties laws of the United States.  We urge all persons who are responsible for the accuracy and
adequacy of the disclosure in the filing  to be certain that the filing include  the information the
Securities Exchange Act of 1934 and all applicable rules requir e.

Sincerely,

 /s/ Jim B. Rosenberg

Jim B. Rosenberg
Senior Assistant Chief  Accountant
Office of Healthcare and Insurance

CORRESP
1
filename1.htm

Correspondence

 Alnylam Pharmaceuticals, Inc.

300 Third Street

 Cambridge, MA
02142

 December 9, 2015

 United States
Securities and Exchange Commission

 Division of Corporation Finance

100 F Street N.E.

 Washington, D.C. 20549

Attention: Jim B. Rosenberg, Senior Assistant Chief Accountant

RE:
Alnylam Pharmaceuticals, Inc.

Form 10-K for Fiscal Year Ended December 31, 2014

Filed February 13, 2015

File No. 001-36407

 Dear Mr. Rosenberg:

This letter is being furnished in response to the comments of the Staff (the “Staff”) of the Securities and Exchange Commission (the
“Commission”) in the Commission’s letter dated November 25, 2015 (the “Comment Letter”) to John M. Maraganore, Ph.D., Chief Executive Officer of Alnylam Pharmaceuticals, Inc. (the “Company”), with respect to
the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2014, and the documents incorporated by reference therein. The responses set forth below have been organized in the same manner in which the Commission’s
comments and headings were organized in the Comment Letter.

 Comment: Notes to Consolidated Financial Statements — 3. Significant Agreements,
page 114

1.
In order to help us understand more fully how your collaborative arrangements impact your financial statements for each period presented, please provide us, in table format, the amounts by year and by line item
included in your statements of operations attributable to transactions arising from collaborative arrangements between you and the other participants and third-parties. Please provide separate tables for each of your significant collaborative
arrangements and for all of your collaborative arrangements in the aggregate (i.e. the significant arrangements and all other arrangements). Present separately amounts with other participants and third-parties that are netted in a financial
statement line item. Refer to ASC 808.

 Mr. Jim B. Rosenberg

U.S. Securities and Exchange Commission

 December 9, 2015

 Page
 2

 Response

The following tables provide the amounts attributable to transactions arising from collaborative arrangements, for each significant arrangement and all other
arrangements, by line item included in the Company’s statements of operations(1):

 Year Ended December 31, 2014

(In thousands)

Takeda

Monsanto

MDCO

Roche/
Arrowhead

Genzyme

Cubist

Isis

Other

Total

 Net revenues from collaborators

$
21,973

$
14,985

$
10,753

$
1,000

$
369

$
—

$
250

$
1,231

$
50,561

 Operating expenses:

 Research and development

—

—

—

—

—

—

9,875

—

9,875

 In-process research and development

—

—

—

—

—

—

—

—

—

 General and administrative

—

—

—

—

—

—

—

—

—

 Restructuring of Tekmira license agreement

—

—

—

—

—

—

—

—

—

 Year Ended December 31, 2013

(In thousands)

Takeda

Monsanto

MDCO

Roche/
Arrowhead

Genzyme

Cubist

Isis

Other

Total

 Net revenues from collaborators

$
21,973

$
5,640

$
4,604

$
—

$
—

$
9,721

$
—

$
5,229

$
47,167

 Operating expenses:

 Research and development

—

—

—

—

—

—

1,483

—

1,483

 In-process research and development

—

—

—

—

—

—

—

—

—

 General and administrative

—

—

—

—

—

—

—

—

—

 Restructuring of Tekmira license agreement

—

—

—

—

—

—

—

—

—

 Year Ended December 31, 2012

(In thousands)

Takeda

Monsanto

MDCO

Roche/
Arrowhead

Genzyme

Cubist

Isis

Other

Total

 Net revenues from collaborators

$
21,973

$
1,954

$
—

$
37,318

$
—

$
2,777

$
—

$
2,703

$
66,725

 Operating expenses:

 Research and development

—

—

—

—

—

—

2,744

—

2,744

 In-process research and development

—

—

—

—

—

—

—

—

—

 General and administrative

—

—

—

—

—

—

—

—

—

 Restructuring of Tekmira license agreement

—

—

—

—

—

—

—

—

—

(1)
There are no transactions with our collaborators that are netted in net revenues from collaborators or operating expenses, including research and development expenses, for the period presented.

* * * *

 The Company
acknowledges that

•

the Company is responsible for the adequacy and accuracy of the disclosure in the filing;

•

staff comments or changes to disclosure in response to staff comments do not foreclose the Commission from taking any action with respect to the filing; and

•

the Company may not assert staff comments as a defense in any proceeding initiated by the Commission or any person under the federal securities laws of the United States.

 Mr. Jim B. Rosenberg

U.S. Securities and Exchange Commission

 December 9, 2015

 Page
 3

 If you have any questions with regard to the Company’s responses or would like to
discuss any of the matters covered in this letter, please contact the undersigned at (617) 551-8200 or Mitchell S. Bloom of Goodwin Procter LLP, the Company’s outside counsel, at (617) 570-1000.

Sincerely,

 /s/ Michael P. Mason

Michael P. Mason

Vice President, Finance and Treasurer

Mail Stop 4720

November 2 5, 2015

VIA E -mail
John M. Maraganore, Ph. D.
Chief Executive Officer
Alnylam Pharmaceuticals, Inc.
300 Third Street ,
Cambridge, MA  02142

Re: Alnylam  Pharmaceuticals, Inc.
 Form 10-K for Fiscal Year Ended December 31, 2014
Filed February 13 , 2015
File No. 001-36407

Dear Dr. Maraganore :

We have limited our review of your filing to the financial statements and related
disclosures and have the following comment .  In our comment, we ask you to provide us with
information so we may better understand your disclosure.

Please respond to this comment within 10 business days by providing the requ ested
information or advise  us as soon as possible  when you will respond .  If you do not believe that
our comment applies to your facts and circumstances, please tell us why in your response.

After reviewing  your response to this comment , we may have additional comments .

Notes to  Consolidate d Financial Sta tements
3. Significant Agreements, page 114

1. In order to help us understand more fully how your collaborative arrangements impact
your financial statements for each period presented, please provide us, in table format, the
amounts  by year and by line ite m included in your statements of operations attributable
to transactions arising from collaborative arrangements between you and the other
participants and third -parties.   Please provide separate tables for each of your significant
collaborative arrangeme nts and for all of your collaborative arrangements in the
aggregate (i.e. the significant arrangements and all other arrangements).  Present
separately amounts with other participants and third -parties that are netted in a financial
statement line item.  R efer to ASC 808.

Dr. John M. Maraganore, Ph.D.
Alnylam Pharmaceuticals, Inc.
November 2 5, 2015
Page 2

 We urge all persons who are responsible for the accuracy and adequacy of the disclosure
in the filing  to be certain that the filing include s the information the Securities Exchange Act of
1934 and all applicable Exchange Act rules requir e.  Since the company and its management are
in possession of all facts relating to a company’s disclosure, they are responsible for the accuracy
and adequacy of the disclosures they have made.

 In responding to our comment, please provide a written statement from the company
acknowledging that:
 the company is responsible for the adequacy and accuracy of the disclosure in the filing;
 staff comment or changes to disclosure in response to staff comment do not foreclose the
Commission from taking any act ion with respect to the filing; and
 the company may not assert staff comment as a defense in any proceeding initiated by the
Commission or any person under the federal securities laws of the United States.

You may contact Bonnie Baynes, Staff Accountant, at (202) 551 -4924  or Mary Mast,
Senior Staff Accountant, at (202) 551 -3613  if you have questions regarding this comment.  In
this regard, do not hesitate to contact me at (202) 551 -3679.

Sincerely,

 /s/ Jim B. Rosenberg

Jim B. Rosenberg
Senior Assistant Chief  Accountant
Office of Healthcare and Insurance

January 14, 2014

Via E -mail
John M. Maraganore, Ph.D.
Chief Executive Officer
Alnylam Pharmaceuticals, Inc.
300 Third Street
Cambridge, MA 02142

Re: Alnylam Pharmaceuticals, Inc.
 Form 10-K for the fiscal year ended December 31, 2012
Filed February 19, 2013
File No. 000 -50743

Dear Dr. Maraganore :

We have completed our review of your filing .  We remind you that our comments or
changes to disclosure in response to our comments do not foreclose the Commission from taking
any action with respect to the company or the filing and the company may not assert staff
comments as a defense in any proceeding initiated by the Commission or any person under the
federal securities laws of the Un ited States.  We urge all persons who are responsible for the
accuracy and adequacy of the disclosure in the filing to be certain that the filing includes the
information the Securities Exchange Act of 1934 and all applicable rules require.

Sincerely,

 /s/ Jeffrey P. Riedler

Jeffrey P. Riedler
Assistant Director

CORRESP
1
filename1.htm

Response Letter

 Alnylam Pharmaceuticals, Inc.

300 Third Street

 Cambridge, MA
02142

 December 17, 2013

 United States
Securities and Exchange Commission

 Division of Corporation Finance

100 F Street N.E.

 Washington, D.C. 20549

Attention: Jeffrey P. Riedler, Assistant Director

RE:
Alnylam Pharmaceuticals, Inc.

 Form 10-K for Fiscal Year Ended December 31, 2012

Filed February 19, 2013

File No. 000-50743

 Dear Mr. Riedler:

This letter is being furnished in response to the comments of the Staff (the “Staff”) of the Securities and Exchange Commission (the
“Commission”) in the Commission’s letter dated December 2, 2013 (the “Comment Letter”) to John M. Maraganore, Ph.D., Chief Executive Officer of Alnylam Pharmaceuticals, Inc. (the “Company”), with
respect to the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2012 and the documents incorporated by reference therein. The responses set forth below have been organized in the same manner in which the
Commission’s comments and headings were organized in the Comment Letter.

 Comment 1: ALN-VSP — Liver Cancer, page 13

1.
We note the disclosure on page 14 indicating that you have a license agreement with Ascletis. Please disclose the material terms of this agreement under a separate caption, including the patents licensed under this
agreement and how they apply to your products, all other material rights and obligations of both parties, the duration, material termination provisions, payment provisions and prior and potential future payments. Additionally, please file this
agreement as an exhibit pursuant to Item 601(b)(10) of Regulation S-K. Alternatively, please provide us with an analysis supporting your determination that you are not substantially dependent upon this agreement.

Response 1

 The Company analyzes each of
its agreements for materiality when it enters into the agreement and periodically thereafter. Item 601(b)(10)(ii)(B) of Regulation S-K clarifies that if an agreement is such as ordinarily accompanies the kind of business conducted by the
registrant, it will be deemed to be made in the ordinary course of business, and therefore not required to be filed, unless the agreement is, among other things, one “upon which the registrant’s business is substantially dependent.”
With respect to the Company’s agreement with Ascletis Pharmaceuticals (Hangzhou) Co., Ltd. (“Ascletis”), the Company has concluded that its agreement with Ascletis was made in the ordinary course of the Company’s business and
that its business is not substantially dependent on the agreement, and accordingly, the Company has not filed this agreement as an exhibit under Item 601(b)(10) of Regulation S-K.

 Mr. Jeffrey P. Riedler

U.S. Securities and Exchange Commission

 December 17, 2013

Page 2

 The Company is a biopharmaceutical company seeking to develop and commercialize novel
therapeutics based on RNA interference (“RNAi”). As part of its collaboration strategy, the Company seeks to enter into co-development and/or worldwide or specific geographic partnerships for specific RNAi therapeutic programs in the
ordinary course of business. Certain of these agreements may be material to the Company due to a combination of various factors, including the amount of any upfront payment, the amount of research and development funding support, the stage of the
research and development program that is the subject of the agreement, the potential future milestone and royalty revenue amounts, and the geographic scope of the collaboration, among other factors. The Ascletis agreement is a regional agreement
that provides rights to Ascletis to develop and commercialize the Company’s therapeutic candidate, ALN-VSP, at its own expense in a limited geographic region. Under the Ascletis agreement, there was no upfront payment and there are modest
development and sales milestone payments and royalty rates, no co-development obligations, and no obligation on the part of Ascletis to provide the Company with development assistance or specific expertise outside of its limited geographic region.
Moreover, the Company is not currently advancing ALN-VSP, the program that is the subject of the Ascletis Agreement, outside of the Ascletis territory until it identifies an additional partner for such territory.

The Ascletis agreement does not fall within any of the enumerated categories under Item 601(b)(10)(ii)(B) of Regulation S-K that would disqualify it from the ordinary course exception. Notwithstanding the Company’s determination that the Ascletis agreement is not material under Item 601(b)(10) of
Regulation S-K, the Company believes that disclosure of this agreement in its Form 10-K and other filings provides meaningful information for investors regarding the Company’s third-party collaboration efforts. Further, given the
Company’s assessment regarding the materiality of the Ascletis agreement, it does not believe that a separately-captioned section describing additional terms of this agreement is necessary to provide investors sufficient information regarding
the agreement.

 Comment 2: Medtronic, page 19

2.
We note that you entered into a collaboration agreement with Medtronic. Please disclose the milestone payments paid to date and aggregate potential milestone payments that may be paid in the future. Please revise
your disclosure to provide information about the royalty rate. For example, you may either provide a range of royalties within ten percent or a statement that the percentage is in the teens, twenties, etc. Additionally, please provide more precise
information about the royalty term by stating the years during which the relevant patents will expire in each relevant jurisdiction.

Response 2

 To date, the Company has not
made any milestone payments to Medtronic, Inc., (“Medtronic”). In addition, to the extent the Company is required to make milestone or royalty payments under this agreement, such payments will not represent a material percentage of its
operating expenses or cash, cash equivalents and marketable securities. Accordingly, the Company does not believe that the payment of development or sales milestone payments to Medtronic would be material to the Company’s results of operations
or financial condition.

 Mr. Jeffrey P. Riedler

U.S. Securities and Exchange Commission

 December 17, 2013

Page 3

 In addition, in April 2012, the Company elected to opt out of the one development program
under its agreement with Medtronic. At this time, the Company has no responsibility for development or costs related to this program, and is only responsible to supply product to Medtronic at cost as well as technical support as requested. As noted
in the Company’s response to Comment No. 1 above, the Company analyzes each of its agreements for materiality when it enters into the agreement and periodically thereafter. At this time, given the change of the Company’s involvement
in development under the Medtronic Agreement, the Company has reassessed the materiality of its agreement with Medtronic and concluded that such agreement was made in the ordinary course of the Company’s business and that its business is not
currently substantially dependent on this agreement, and accordingly, the Company does not intend to continue to file this agreement as an exhibit to its Form 10-K for the year ended December 31, 2013 under Item 601(b)(10) of Regulation
S-K. Notwithstanding the Company’s determination that the Medtronic Agreement is no longer material under Item 601(b)(10) of Regulation S-K, the Company believes that disclosure of this agreement in its Form 10-K and other filings provides
meaningful information for investors regarding the Company’s third-party collaboration efforts. Further, given the Company’s assessment regarding the materiality of the Medtronic agreement, it does not believe that additional disclosure of
the terms of this agreement is necessary to provide investors sufficient information regarding the agreement.

 Comment 3: The Medicines Company,
page 22

3.
We note that you entered into a license agreement with MedCo. Please revise your disclosure to provide more precise information about the royalty rate. For example, you may either provide a range of royalties within
ten percent or a statement that the percentage is in the teens, twenties, etc. Additionally, please file this agreement as an exhibit pursuant to Item 601(b)(10) of Regulation S-K. Alternatively, please provide us with an analysis supporting
your determination that you are not substantially dependent upon this agreement.

 Response 3

The Company executed the license agreement with The Medicines Company (“MDCO”) on February 13, 2013. The agreement was
originally filed as an exhibit pursuant to Item 601(b)(10) of Regulation S-K to the Company’s Form 10-Q for the quarter ended March 31, 2013 and re-filed as an exhibit to the Company’s Form 10-Q/A for the quarter ended
March 31, 2013 to respond to the Staff’s comments on the Company’s Confidential Treatment Request.

 In
response to the Staff’s comment regarding disclosure of more precise information about the royalty rate of the license agreement with MDCO, the Company intends to include revised disclosure regarding the MDCO agreement in its future filings
with the Commission, including its Form 10-K for the year ended December 31, 2013, and to continue to file the agreement as an exhibit to its Form 10-K until such time as the Company determines that this agreement is no longer
material as provided under Item 601(b)(10) of Regulation S-K . The revised disclosure will be substantially similar to that set forth below:

“The Medicines Company. In February 2013, we and MDCO entered into a license and collaboration agreement pursuant to which we
granted to MDCO an exclusive, worldwide license to develop, manufacture and commercialize RNAi therapeutics targeting PCSK9, including ALN-PCS02 and ALN-PCSsc, for the treatment of hypercholesterolemia and other human diseases. In consideration for
the rights granted to MDCO under the MDCO agreement, MDCO paid us an

 Mr. Jeffrey P. Riedler

U.S. Securities and Exchange Commission

 December 17, 2013

Page 4

upfront cash payment of $25.0 million. In addition, MDCO is required to make payments to us upon the achievement of specified clinical development, regulatory approval and commercialization
milestones totaling up to $180.0 million. In addition, the Company will be entitled to royalties ranging from the low- to high- teens, based on annual worldwide net sales, if any, of ALN-PCS Licensed
Products by MDCO, its affiliates and sublicensees, subject to reduction under specified circumstances.

 Due to the uncertainty of
pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any milestone or royalty payments from MDCO.

Under the MDCO agreement, we and MDCO will collaborate in the further development of licensed products. We will retain responsibility for the
development of licensed products until Phase I completion, as defined in the MDCO agreement, at our cost, up to an agreed upon initial development cost cap. MDCO will assume all other responsibility for the development and commercialization of
licensed products, at its sole cost. Initially the collaboration included the development of both ALN-PCS02 and ALN-PSCsc in parallel. In October 2013, the parties announced the selection of ALN-PCSsc for ongoing development, in accordance with the
terms of the MDCO agreement. The collaboration between us and MDCO will be governed by a joint steering committee that will be comprised of an equal number of representatives from each party.

We will be solely responsible for obtaining supply of finished product reasonably required for the conduct of our obligations under the initial
development plan through Phase I completion, and supplying MDCO with finished product reasonably required for the first Phase II clinical trial of a licensed product conducted by MDCO, at our expense, provided such costs do not exceed the
development costs cap, subject to certain exceptions. After such time, MDCO will have the sole right and responsibility to manufacture and supply licensed product for development and commercialization under the MDCO development plan, subject to the
terms of the MDCO agreement. We and MDCO intend to enter into a supply and technical transfer agreement to provide for supply of licensed products to MDCO within a specified time following the effective date of the MDCO agreement.

Unless terminated earlier in accordance with the terms of the agreement, the MDCO agreement expires on a licensed product-by-licensed product
and country-by-country basis upon expiration of the last royalty term for any licensed product in any country, where a royalty term is defined as the latest to occur of (1) the expiration of the last valid claim of patent rights covering a
licensed product, (2) the expiration of the Regulatory Exclusivity, as defined in the MDCO agreement, and (3) the twelfth anniversary of the first commercial sale of the licensed product in such country. We estimate that our fundamental
RNAi patents covering licensed products under the MDCO agreement will expire both in and outside of the United States generally between 2015 and 2023. We also estimate that our ALN-PCS product-specific patents covering licensed products under the
MDCO agreement in the United States and elsewhere will expire at the end of 2033. These patent rights are subject to potential patent term extensions and/or supplemental protection certificates extending such terms in countries where such extensions
may become available. In addition, more patent filings relating to the collaboration may be made in the future.

 Mr. Jeffrey P. Riedler

U.S. Securities and Exchange Commission

 December 17, 2013

Page 5

 Either party may terminate the MDCO agreement in the event the other party fails to cure a
material breach or upon patent-related challenges by the other party. We may terminate the agreement in the event that a lead licensed product has not been designated by the joint steering committee within a designated time period. In addition, MDCO
has the right to terminate the agreement without cause at any time upon four months’ prior written notice.

 During the term of the
MDCO agreement, neither party will, alone or with an affiliate or third party, research, develop or commercialize, or grant a license to any third party to research, develop or commercialize, in any country, any product directed to the PCSK9 gene,
other than a licensed product, without the prior written agreement of the other party, subject to the terms of the MDCO agreement.”

 Comment 4:
Arrowhead, page 24

4.
We note that you have a collaboration agreement with Arrowhead. Please disclose the material terms of this agreement under a separate caption, including the patents licensed under this agreement and how they apply to
your products, all other material rights and obligations of both parties, the duration, material termination provisions, and payment terms and the prior and potential future payments. Additionally, please file this agreement as an exhibit pursuant
to Item 601(b)(10) of Regulation S-K. Alternatively, please provide us with an analysis supporting your determination that you are not substantially dependent upon this agreement.

Response 4

 As discussed in the
Company’s response to Comment No. 1 above, the Company analyzes each of its agreements for materiality when it enters into the agreement and periodically thereafter. The Company has determined that its agreement with Arrowhead Research
Corporation (“Arrowhead”) is not a material contract required to be filed as an exhibit under Item 601(b)(10) of Regulation S-K. Item 601(b)(10)(ii)(B) of Regulation S-K clarifies that if an agreement is such as ordinarily
accompanies the kind

CORRESP
1
filename1.htm

Correspondence

 December 9, 2013

Via EDGAR

 Securities and Exchange Commission

100 F Street, N.E.

 Washington, DC 20549

Attention: Jeffrey P. Riedler, Assistant Director

RE:
Alnylam Pharmaceuticals, Inc.

 Form 10-K for Fiscal Year Ended December 31, 2012

 Filed February 19, 2013

File No. 000-50743

 Ladies and Gentlemen:

 Alnylam Pharmaceuticals, Inc. (the “Company”) hereby advises the staff (the “Staff”) of the Securities
and Exchange Commission (the “Commission”) that the Company has received the Staff’s letter dated December 2, 2013 (the “Comment Letter”), regarding the Commission’s review of the Company’s
Annual Report on Form 10-K for the fiscal year ended December 31, 2012. The Comment Letter requests that the Company respond within ten (10) business days from the date thereof, or inform the Staff of when the Company would provide a
response. As discussed by Matthew Jones of the Commission with Mitchell Bloom, the Company’s outside counsel at Goodwin Procter LLP, the Company respectfully requests an extension of an additional ten (10) business days until
December 31, 2013 to respond to the Comment Letter. The Company is committed to responding to the Comment Letter promptly and intends to provide a response to the Staff no later than December 31, 2013. Should you have any questions
regarding the request made herein, please do not hesitate to contact me at (617) 551-8200. Thank you very much for your courtesy and cooperation in this matter.

Sincerely,

 /s/ Michael P. Mason

Michael P. Mason

Vice President, Finance and Treasurer

cc:
Mitchell S. Bloom – Goodwin Procter LLP

December 2, 2013

Via E -mail
John M. Maraganore, Ph.D.
Chief Executive Officer
Alnylam Pharmaceuticals, Inc.
300 Third Street
Cambridge, MA 02142

Re: Alnylam Pharmaceuticals, Inc.
 Form 10-K for the fiscal year ended December 31, 2012
Filed February 19, 2013
File No. 000-50743

Dear Dr. Maraganore :

We have reviewed your filing an d have the following comments.  In some of our
comments, we may ask you to provide us with information so  we may better understand your
disclosure.

Please respond to this letter within ten business days by amending your filing, by
providing the requested information, or by advising us when you will provide the requested
response.   If you do not believe our c omments apply to your facts and circumstances or do not
believe an amendment is appropriate, please tell us why in your response.

After reviewing any amendment to your filing and the information you provide in
response to these  comments, we may have  additional comments.

ALN -VSP — Liver Cancer, page 13

1. We note the disclosure on page 14 indicating tha t you have a license agreement with
Ascletis . Please disclose the material terms of this agreement under a separate caption,
including the patents licensed under this agreement and how they apply to your products,
all other material rights and obligations of both parties, the duration, material termination
provisions, payment provisions  and prior and potential future payments. Additionally,
please file this agreement as an exhibit pursuant to Item 601(b)(10) of Regulation S -K.
Alternatively, please provide us with an analysis supporting your determination that you
are not substantially dependent upon this agreement.

Medtronic, page 19

2. We no te that you entered into a collaboration agreement with Medtronic.  Please  disclose
the milestone payments paid to date  and aggregate potential milestone payments that may

John M. Maraganore, Ph.D.
Alnylam Pharmaceuticals, Inc.
December 2, 2013
Page 2

 be paid in the future. Please  revise your disclosure to provide information about the
royalty rate. For example, you may either provide a range of royalties within ten percent
or a statement that the percentage is in the teens, twenties, etc.  Additionally, p lease
provide more precise information about the royalty term by stating the years during
which the relevant patents will expire in each relevant jurisdiction.

The Medicines Company, page 22

3. We note that you entered into a license agreement with MedCo.  Please  revise your
disclosure to provide more precise information about the royalty  rate. For example, you
may either provide a range of royalties within ten percent or a statement that the
percentage is in the teens, twenties, etc.  Additionally, please file this agreement as an
exhibit pursuant to Item 601(b)(10) of Regulation S -K. Alte rnatively, please provide us
with an analysis supporting your determination that you are not substantially dependent
upon this agreement .

Arrowhead, page 24

4. We note that you have a collaboration  agreement with Arrowhead . Please disclose the
material ter ms of this agreement under a separate caption, including the patents licensed
under this agreement and how they apply to your products, all other material rights and
obligations of both parties, the duration, material termination provisions, and payment
terms and the prior and potential future payments. Additionally, please file this agreement
as an exhibit pursuant to Item 601(b)(10) of Regulation S -K. Alternatively, please
provide us with an analysis supporting your determination that you are not substantially
dependent upon this agreement .

Tekmira, page 24

5. We note your reference in the third full paragraph on page 25 to a significant buy down
of milestone payments and a reduction of royalty rates payable to Tekmira resulting from
the 2012 cross -licensing agreement. Please provide a range for the reduced roya lty rate
within ten percent.

We urge all persons who are responsible for the accuracy and adequacy of the disclosure
in the filing to be certain that the filing includes the information the Securities Exchange Act of
1934 and all applicable Exchange Act rules require.   Since the company and its management are
in possession of all facts relating to a company’s disclosure, they are responsible for the accuracy
and adequacy of the disclosures they have made.

 In responding to our comments, please provide  a written statement from the company
acknowledging that:

 the company is responsible for the adequacy and accuracy of the disclosure in the filing;

John M. Maraganore, Ph.D.
Alnylam Pharmaceuticals, Inc.
December 2, 2013
Page 3

 staff comments or changes to disclosure in response to staff comments do not foreclose
the Commission from taking any action with respect to the filing; and

 the company may not assert staff comments as a defense in any proceeding initiated by
the Commission or any person under the federal securities laws of the United States.

Please contact Matthew Jones  at (202) 551 -3786 or me at (202) 551 -3715 with any other
questions.

Sincerely,

 /s/ Jeffrey P. Riedler

Jeffrey P. Riedler
Assistant Director

March 23, 2011

John M. Maraganore, Ph.D. Chief Executive Officer Alnylam Pharmaceuticals, Inc. 300 Third Street
Cambridge, MA 02142

Re: Alnylam Pharmaceuticals, Inc.  Form 10-K
Filed February 26, 2010 File No. 000-50743
 Dear Mr. Maraganore:
We have completed our review of your fili ng and do not have any further comments at
this time.
Sincerely,
     Jeffrey Riedler
Assistant Director

CORRESP
1
filename1.htm

corresp

March 10, 2011

By EDGAR Transmission

Securities and Exchange Commission

Division of Corporate Finance

100 F Street, N.E.

Washington, D.C. 20549

Attention: Johnny Gharib

    Re:

    Alnylam Pharmaceuticals, Inc.

    Form 10-K

    Filed February 26, 2010

    File No. 000-50743

    Ladies and Gentlemen:

On behalf of Alnylam Pharmaceuticals, Inc. (the “Company”), I am writing in response to comments
contained in the letter dated February 28, 2011 (the “Letter”) from Jeffrey Riedler of the Staff
(the “Staff”) of the Securities and Exchange Commission (the “Commission”) to John M. Maraganore,
the Company’s Chief Executive Officer. The responses set forth below are keyed to the numbering of
the comments and the headings used in the Letter.

Proxy Statement on Schedule 14A, filed April 20, 2010

2009 Annual Incentive Program, page 26

    1.

    We note your response to our prior comment 4 and your disclosure that the company has not
disclosed Ms. Allen’s performance target with respect to specified internal operating expense
levels under its annual operating plan because the company believes that this information
constitutes confidential financial data, the disclosure of which would result in competitive
harm to it. However, you have already disclosed your operating expenses in your 2010 10-K
filed on February 18, 2011. Please revise your disclosure to include a discussion of Ms.
Allen’s performance target with respect to specified internal operating expense levels and
compare them to the level of operating expenses incurred by the company.

    Response:

    In response to the Staff’s comment, the Company has revised the disclosure
regarding Ms. Allen’s individual objectives to include a discussion of Ms. Allen’s
performance target with respect to specified internal operating expense levels. The
Company notes that it has not provided a comparison of this performance target to the
level of GAAP operating expenses disclosed in the Company’s Annual Report on Form 10-K
for the year ended December 31, 2010, as these measures are not the same. As
previously noted by the Company, multiple factors go into determining the Company’s
operating plan,

Securities and Exchange Commission

March 10, 2011

Page 2

    which contains financial targets and budgets that are used to guide the
operations of the Company. The Company has included in its revised
disclosure below an explanation of the distinction between its internal
operating expense levels under its annual operating plan and its reported
GAAP operating expenses for 2010. The Company intends to include revised
disclosure regarding Ms. Allen’s individual objectives and performance in its
2011 proxy statement substantially similar to that set forth below:

“Ms. Allen’s individual objectives were focused on meeting specified financial goals, including
meeting internal operating expense levels of no more than $110 million under our annual operating
plan, and year-end minimum cash balance requirements of greater than $340 million (excluding a
potential one-time license payment from a collaborator) ([ ]%), supporting business development
efforts to establish strategic alliances to fund our business ([ ]%), managing our investment
portfolio ([ ]%) and managing the audit of our financial statements, along with various public
reporting obligations and tax matters ([ ]%), and achieving specified metrics with respect to the
information technology and facilities groups ([ ]%). Ms. Allen’s goals relating to internal
operating expense levels were based upon our annual operating plan. Multiple factors go into
determining our operating plan, which contains financial targets and budgets that we use to guide
our operations. Internal operating expenses do not align with reported GAAP operating expenses, as
they consist primarily of cash operating expenses and exclude items such as depreciation and
stock-based compensation. Our compensation committee also considered both Dr. Maraganore’s and Mr.
Greene’s recommendations with respect to Ms. Allen’s performance. Our compensation committee
determined that Ms. Allen achieved [ ]% of her individual objectives for 2010, including meeting
year-end internal operating expense levels of no more than $110 million under our annual operating
plan and achievement of internal year-end cash balance objectives of greater than $340 million,
ending 2010 with $350 million. Our compensation committee determined that under the 2010 annual
incentive program, Ms. Allen earned a cash incentive award of $[ ], representing [ ]% of her
target cash award opportunity, reduced by the corporate performance modifier of [ ]%.”

If you require additional information, please telephone either the undersigned at (617) 551-8200,
or Lia Der Marderosian of WilmerHale, the Company’s outside counsel, at (617) 526-6000.

Very truly yours,

/s/ Michael P. Mason

Michael P. Mason

Vice President, Finance and Treasurer

    cc:

    Philip T. Chase, Esq.

    Lia Der Marderosian, Esq.

February 28, 2011

John M. Maraganore, Ph.D. Chief Executive Officer Alnylam Pharmaceuticals, Inc. 300 Third Street
Cambridge, MA 02142

Re: Alnylam Pharmaceuticals, Inc.  Form 10-K
Filed February 26, 2010 File No. 000-50743
 Dear Mr. Maraganore:
 We have reviewed your response letter date d February 18, 2011 and have the following
comment.
 Please respond to this letter within te n business days by providing the requested
information, or by advising us when you will provide the requested response.  If you do not believe our comment applies to your facts and circumstances, please tell us why in your response.
 After reviewing the information you provide in  response to this comment, we may have
additional comments.
Proxy Statement on Schedule 14A, filed April 20, 2010

2009 Annual Incentive Program, page 26

1. We note your response to prior comment 4 a nd your disclosure that the company has
not disclosed Ms. Allen’s pe rformance target with resp ect to specified internal
operating expense levels under its annual operating plan because the company
believes that this information constitutes confidential financial data, the disclosure of which would result in competitive harm to it.  However, you have already disclosed your operating expenses in your 2010 10-K filed on February 18, 2011. Please revise
your disclosure to include a di scussion of Ms. Allen’s perf ormance target with respect
to specified internal operating expense le vels and compare them to the level of
operating expenses incurred by the company.

John M. Maraganore, Ph.D. Alnylam Pharmaceuticals, Inc. February 28, 2011 Page 2

You may contact Johnny Gharib  at (202) 551-3170 or me at  (202) 551-3715 if you have
any questions.
Sincerely,
       Jeffrey Riedler
Assistant Director

CORRESP
1
filename1.htm

corresp

February 18, 2011

By EDGAR Transmission

Securities and Exchange Commission

Division of Corporate Finance

100 F Street, N.E.

Washington, D.C. 20549

Attention: Johnny Gharib

    Re:

    Alnylam Pharmaceuticals, Inc.

Form 10-K

Filed February 26, 2010

File No. 000-50743

Ladies and Gentlemen:

On behalf of Alnylam Pharmaceuticals, Inc. (the “Company”), I am writing in response to comments
contained in the letter dated February 11, 2011 (the “Letter”) from Jeffrey Riedler of the Staff
(the “Staff”) of the Securities and Exchange Commission (the “Commission”) to John M. Maraganore,
the Company’s Chief Executive Officer. The responses set forth below are keyed to the numbering of
the comments and the headings used in the Letter.

Form 10-K, filed February 26, 2010

Business, page 2

    1.

    We note your response to our prior comment 1 and your disclosure regarding your license
agreement with Max Planck Innovation that you will be required to pay future royalties on net
sales of all therapeutic and prophylactic products. Please revise your disclosure to include
a range of royalty rates not to exceed ten percent. An acceptable range of royalties is one
of the following: “single-digits,” “teens,” “twenties,” etc.

    Response:

    In response to the Staff’s comment, the Company has revised its disclosure
regarding its license agreement with Max Planck Innovation to include a range of
royalty rates. The Company intends to include revised disclosure in its Form 10-K for
the year ended December 31, 2010 substantially similar to that set forth below:

“In December 2002, we entered into a co-exclusive license with Max Planck Innovation for the
worldwide rights to use and sublicense certain patented technology to develop and commercialize
therapeutic products and related applications. We also obtained the rights to use, without the
right to sublicense, the technology for all diagnostic uses other than for the purposes of
therapeutic monitoring. In consideration for the rights to license this technology, we issued to
Max Planck

Page 2

Innovation 723,240 shares of Series B redeemable convertible preferred stock with a fair value of
$1.8 million. We were also given the right to acquire the remaining 50% exclusive rights, which
right we exercised upon our acquisition of Ribopharma AG in July 2003. In consideration for the
remaining rights to this technology, we issued Max Planck Innovation an additional 158,605 shares
of Series B redeemable convertible preferred stock with a fair value of $0.4 million. The 881,845
shares of Series B redeemable convertible preferred stock held by Max Planck Innovation converted
into 464,128 shares of common stock upon the closing of our initial public offering in June 2004.

In June 2005, we entered into an amendment to our agreement with Max Planck Innovation that secured
our exclusivity to use and sublicense certain patented technology to develop and commercialize
therapeutic products and related applications. In connection with this amendment, we issued
270,000 shares of our common stock, which were valued at $2.1 million, to Max Planck Innovation and
certain of its affiliated entities.

We are not obligated to pay any development or sales milestone payments to Max Planck Innovation,
however, we will be required to pay Max Planck Innovation future
single-digit royalties on
net sales of all therapeutic and prophylactic products developed with the technology, if any.

Our agreements with Max Planck Innovation generally remain in effect until the expiration of the
last-to-expire patent licensed thereunder. We estimate that the principal issued patents covered
under the Max Planck Innovation agreements will expire both in and outside the United States during
2021, subject to any potential patent term extensions, restoration and/or supplemental protection
certificates extending such term extensions in countries where such extensions may become
available. We may terminate the agreements without cause with six months’ prior notice to Max
Planck Innovation, and Max Planck Innovation may terminate the agreements in the event that we
materially breach our obligations thereunder. Max Planck Innovation also has the right to
terminate the agreements in the event that we, independently or through a third party, attack the
validity of any of the licensed patents.”

Kyowa Hakko Kirin, page 20

    2.

    We note your response to our prior comment 2 that under the Kyowa Hakko Kirin agreement,
there are modest development and sales milestone payments and royalty rates. However, we also
note in your 2009 Form 10-K that Kyowa Hakko Kirin paid you an upfront cash payment of $15
million and is required to make payments to you upon achievement of specified development
sales milestones totaling up to $78 million in addition to royalty payments based on annual
net sales. These amounts do not appear to be modest given that you had revenues of
approximately $100 million and net losses of approximately $47.6 million in 2009. Please file
as an exhibit to your 2010 Form 10-K, the license and collaboration agreement with Kyowa Hakko
Kirin dated June 2008.

    Response:

    The Company acknowledges the Staff’s comment and intends to file the license and
collaboration agreement with Kyowa Hakko Kirin as an exhibit to its Form 10-K for the
year ended December 31, 2010.

Page 3

Delivery Initiatives, page 24

    3.

    We note your response to our prior comment 3 and your disclosure that Tekmira and Protiva are
eligible to receive royalty payments on annual product sales of each RNAi therapeutic
formulated using Tekmira’s or Protiva’s liposomal delivery formulation technologies, and that
you are eligible to receive royalties on annual sales of RNAi therapeutic products for which
you granted Tekmira and Protiva licenses. Please revise your disclosure to include a range of
royalty rates not to exceed ten percent for royalties that you will pay to and receive from
Tekmira and Protiva. An acceptable range of royalties is one of the following:
“single-digits,” “teens,” “twenties,” etc.

    Response:

    In response to the Staff’s comment, the Company has revised its disclosure
regarding its license agreements with Tekmira and Protiva to include a range of royalty
rates. The Company intends to include revised disclosure in its Form 10-K for the year
ended December 31, 2010 substantially similar to that set forth below:

“In January 2007, we obtained an exclusive worldwide license to the liposomal delivery formulation
technology of Tekmira for the discovery, development and commercialization of LNP formulations for
the delivery of RNAi therapeutics and a non-exclusive worldwide license to certain liposomal
delivery formulation technology of Protiva Biotherapeutics Inc., or Protiva, for the discovery,
development and commercialization of certain LNP formulations for the delivery of RNAi
therapeutics. In May 2008, Tekmira acquired Protiva. In connection with this acquisition, we
entered into new agreements with Tekmira and Protiva, which provide us access to key existing and
future technology and intellectual property for the systemic delivery of RNAi therapeutics with
liposomal delivery technologies. Under these agreements, we continue to have exclusive rights to
the Semple (U.S. Patent No. 6,858,225) and Wheeler (U.S. Patent Nos. 5,976,567 and 6,815,432)
patents for RNAi, which we believe are critical for the use of LNP delivery technology. Under our
agreements with Tekmira and Protiva, Tekmira and Protiva are eligible to receive up to an aggregate
of $16.0 million in milestone payments for each RNAi therapeutic formulated using Tekmira’s or
Protiva’s liposomal delivery formulation technologies, together
with single-digit royalty
payments on annual product sales. In each of 2009 and 2010, we paid $0.5 million in milestone
payments to Tekmira under these license agreements. We charge these milestone payments to research
and development expense.

We are developing ALN-VSP, a systemically delivered RNAi therapeutic, for the treatment of primary
and secondary liver cancer. ALN-VSP contains two siRNAs formulated using a first-generation LNP
formulation developed by Tekmira. We also have rights to use this LNP technology in the advancement
of our other systemically delivered RNAi therapeutic programs, and we are advancing ALN-TTR01, for
the treatment of ATTR, utilizing this first-generation LNP formulation. In parallel with ALN-TTR01,
we are advancing ALN-TTR02 utilizing a second-generation LNP formulation. In addition, we have
published pre-clinical results from development programs for other systemically delivered RNAi
therapeutics, including ALN-PCS, for the treatment of severe hypercholesterolemia. We are also
advancing ALN-PCS using a second-generation LNP formulation.

Page 4

Under our agreements with Tekmira and Protiva, we also granted Tekmira and Protiva three exclusive
and five non-exclusive licenses under our InterfeRx program to develop and commercialize RNAi
therapeutics directed to up to eight gene targets in which we have no direct strategic interest,
including the targets apolipoprotein B and polo-like kinase 1, or PLK1, and a recently granted
license in connection with Tekmira’s research program directed towards the Ebola virus. We are
eligible to receive up to an aggregate of $8.5 million in milestone payments for each RNAi
therapeutic directed to four of these targets, together with
single-digit royalties on
annual sales of RNAi therapeutic products directed to all of these targets, if any. In addition,
under our agreement with Protiva, we have the right to “opt-in” to the Tekmira research program
directed to PLK1 and contribute 50% of product development costs and share equally in any future
product revenues. We have until the start of a Phase II clinical trial in this PLK1 research
program to exercise our opt-in right.

In connection with Tekmira’s acquisition of Protiva, in May 2008, we made an equity investment of
$5.0 million in Tekmira, purchasing 2,083,333 shares of Tekmira common stock at a price of $2.40
per share, which represented a premium of $1.00 per share. In November 2010, Tekmira effected a
one-for-five reverse stock split, after which we own 416,666 shares of Tekmira common stock.

The terms of our agreements with Tekmira and Protiva generally end upon the expiration of the
last-to-expire patent licensed thereunder, whether such patent is a patent licensed by Tekmira or
Protiva to us, or vice versa. As the licenses from Tekmira and Protiva will include additional
patents, if any, filed to cover future inventions, if any, the dates of expiration cannot be
determined at this time. Either we or Protiva may terminate a license it granted to the other in
the event that the other party materially breaches its obligations relating to that license.
Furthermore, either we or Tekmira may terminate our agreements with each other in the event the
other party materially breaches an obligation under those agreements, but such termination will be
limited to a particular product and/or region in the event of a material breach by the other party
that has a material adverse effect only on that particular product in that region.”

Proxy Statement on Schedule 14A, filed April 20, 2010

2009 Annual Incentive Program, page 26

    4.

    We note your response to our prior comment 5 and your disclosure regarding 2010 corporate
goals and individual objectives. We also note your discussion of Ms. Allen’s individual
objectives which are partly focused on meeting specified financial goals, including meeting
specified operating expense levels and minimum cash balance requirements at year-end. These
objectives appear to be quantitative. To the extent that the objectives are quantitative,
please revise your disclosure so that the discussion of objectives and achievements is also
quantitative.

    Response:

    In response to the Staff’s comment, the Company has revised the
disclosure regarding Ms. Allen’s individual objectives to include a
quantitative discussion of the minimum year-end cash requirements. The Company
has not disclosed Ms. Allen’s performance target with respect to specified
internal operating expense levels under its annual operating plan because the
Company believes that this information constitutes confidential financial data, the
disclosure of which would result in competitive harm to it. Each year, the Company
engages in a robust process to establish the operating plan, which contains financial
targets and budgets that are used to guide the operations of the Company. In
developing the operating plan, management considers various factors relating to
its own operations and research and development programs, as well as overall
economic and market conditions. The operating plan is prepared by Company management
and presented to the Board of Directors (the “Board”) for its consideration
and the Board provides feedback to management.

Page 5

    The finalized operating plan that results from this process is then approved by the
Board. The Company has included disclosure that Ms. Allen’s target specified operating
expense levels for 2010 were set at a level that was attainable but difficult to achieve.
The Company intends to include revised disclosure regarding Ms. Allen’s individual
objectives and performance in its 2011 proxy statement substantially similar to that set forth below:

“Ms. Allen’s individual objectives were
focused on meeting specified financial goals, including meeting specified internal operating expense
levels under our annual operating plan within 5% of target, which we believe were set at
levels that were attainable but aggressively established, and year-end minimum cash balance
requirements of greater than $340.0 million (excluding a potential one-time license payment from a collaborator)
([  ]%), supporting business development efforts to establish strategic alliances to fund our
business ([  ]%), managing our investment portfolio ([  ]%) and managing the audit of our financial
statements, along with various public reporting obligations and tax matters ([  ]%), and achieving
specified metrics with respect to the information technology and facilities groups ([  ]%). Our
compensation committee also considered both Dr. Maraganore’s and Mr. Greene’s recommendations with
respect to Ms. Allen’s performance.  Our compensation committee determined that Ms. Allen achieved [  ]%
of her individual objectives for 2010, including meeting specified year-end internal operating expense
levels under our annual operating plan and achievement of internal year-end cash balance objectives
of greater than $340.0 million, ending 2010 with $350.0 million.  Our compensation committee determined
that under the 2010 annual incentive program, Ms. Allen earned a cash incentive award of $[  ],
representing [  ]% of her target cash award opportunity, reduced by
the corporate performance modifier of [  ]%.”

If you require additional information, please telephone either the undersigned at (617) 551-8200,
or Lia Der Marderosian of WilmerHale, the Company’s outside counsel, at (617) 526-6000.

Very truly yours,

/s/ Patricia L. Allen

Patricia L. Allen

Vice President of Finance and Treasurer

    cc:

    Philip T. Chase, Esq.

Lia Der Marderosian, Esq.

February 11, 2011

John M. Maraganore, Ph.D. Chief Executive Officer Alnylam Pharmaceuticals, Inc. 300 Third Street
Cambridge, MA 02142

Re: Alnylam Pharmaceuticals, Inc.  Form 10-K
Filed February 26, 2010 File No. 000-50743
 Dear Mr. Maraganore:
 We have reviewed your response letter da ted January 12, 2011 and have the following
comments.
 Please respond to this letter within te n business days by providing the requested
information, or by advising us when you will provide the requested response.  If you do not believe our comments apply to your facts and circum stances, please tell us w hy in your response.
 After reviewing the information you provide in response to these comments, we may
have additional comments.
Form 10-K, filed February 26, 2010

Business, page 2

1. We note your response to our prior comment 1 and your disclosure regarding your license agreement with Max Planck Innovation that you will be required to pay future royalties
on net sales of all therapeutic and prophylactic products.  Please revise your disclosure to
include a range of royalty rates not to ex ceed ten percent.  An acceptable range of
royalties is one of the following: “single-digits,” “teens,” “twenties,” etc.
 Kyowa Hakko Kirin, page 20

2. We note your response to our prior comme nt 2 that under the Kyowa Hakko Kirin
agreement, there are modest development and sa les milestone payments and royalty rates.
However, we also note in your 2009 Form  10-K that Kyowa Hakko Kirin paid you an
upfront cash payment of $15 million and is required to make payments to you upon
achievement of specified development sales milestones totaling up to $78 million in addition to royalty payments based on annual net sales.  These amounts do not appear to

John M. Maraganore, Ph.D. Alnylam Pharmaceuticals, Inc. February 11, 2011 Page 2

be modest given that you had revenues of approximately $100 million and net losses of
approximately $47.6 million in 2009.  Please file  as an exhibit to your 2010 Form 10-K,
the license and collaboration agreement with Kyowa Haddo Ki rin dated June 2008.

Delivery Initiatives, page 24

3. We note your response to our prior comment 3 and your disclosure that Tekmira and
Protiva are eligible to receive royalty pa yments on annual product sales for each RNAi
therapeutic formulated using Tekmira’s or Protiva’s liposomal delivery formulation
technologies, and that you ar e eligible to receive royal ties on annual sales of RNAi
therapeutic products for which you granted Tekm ira and Protiva licenses.  Please revise
your disclosure to include a ra nge of royalty rates not to ex ceed ten percent for royalties
that you will pay to and receive from Tekm ira and Protiva.  An acceptable range of
royalties is one of the fo llowing: “single-digits,” “teens,” “twenties,” etc.

Proxy Statement on Schedule 14A, filed April 20, 2010
 2009 Annual Incentive Program, page 26

4. We note your response to our prior comme nt 5 and your disclosure regarding 2010
corporate goals and individual objectives.  We also note your  discussion of Ms. Allen’s
individual objectives which are partly fo cused on meeting specified financial goals,
including meeting specified operating expense levels and minimum cash balance requirements at year-end.  These objectives appe ar to be quantitative.  To the extent that
the objectives are quantitative, please revise  your disclosure so that the discussion of
objectives and achievements is also quantitative.
 You may contact Johnny Gharib  at (202) 551-3170 or me at  (202) 551-3715 if you have
any questions.
Sincerely,
       Jeffrey Riedler
Assistant Director

CORRESP
1
filename1.htm

corresp

January 12, 2011

By EDGAR Transmission

Securities and Exchange Commission

Division of Corporate Finance

100 F Street, N.E.

Washington, D.C. 20549

Attention: Johnny Gharib

    Re:

    Alnylam Pharmaceuticals, Inc.

Form 10-K

Filed February 26, 2010

File No. 000-50743

Ladies and Gentlemen:

On behalf of Alnylam Pharmaceuticals, Inc. (the “Company”), I am writing in response to comments
contained in the letter dated December 2, 2010 (the “Letter”) from Jeffrey Riedler of the Staff
(the “Staff”) of the Securities and Exchange Commission (the “Commission”) to John M. Maraganore,
the Company’s Chief Executive Officer. The responses set forth below are keyed to the numbering of
the comments and the headings used in the Letter.

Form 10-K, filed February 26, 2010

Business, page 2

    1.

    We note that you have included as exhibits various license agreements with each of Cancer
Research Technology Limited, Carnegie Institution of Washington, Cold Spring Harbor
Laboratory, Garching Innovation GmbH (now known as Max Planck Innovation GmbH) and The Board
of Trustees of the Leland Stanford Junior University. Please describe the material terms of
each of these agreements, including, but not limited to any payment provisions, a range of
royalty rates, aggregate milestones, usage restrictions, exclusivity provisions and duration
and termination provisions.

              Response:

    The Company analyzes each of its agreements for materiality when it enters into
the agreement and periodically thereafter. Item 601(b)(10)(ii)(B) of Regulation S-K
clarifies that if an agreement is such as ordinarily accompanies the kind of business
conducted by the registrant, it will be deemed to be made in the ordinary course of
business, and therefore not required to be filed, unless the agreement is, among other
things, one “upon which the registrant’s business is substantially dependent.” The
Company has reassessed the materiality of its agreements with each of Cancer Research
Technology Limited (“CRT”), Carnegie Institution of Washington

300 Third Street • Cambridge MA, 02142 • main 617.551.8200 • fax 617.551.8101 •

www.alnylam.com

Securities and Exchange Commission

January 12, 2011

Page 2

    (“Carnegie”), Cold Spring Harbor Laboratory (“Cold Spring”) and The Board of
Trustees of the Leland Stanford Junior University (“Stanford”) and concluded
that each such agreement was made in the ordinary course of the Company’s
business and that its business is not currently substantially dependent on
any one of these agreements, and accordingly, the Company does not intend to
continue to file any of these agreements as an exhibit to its Form 10-K for
the year ended December 31, 2010 under Item 601(b)(10) of Regulation S-K.
The Company continues to consider its license agreements with Garching
Innovation GmbH (now known as Max Planck Innovation GmbH) (“Max Planck”)
material agreements. The Company intends to revise its disclosure regarding
the Max Planck license agreements in its Form 10-K for the year ended
December 31, 2010 and to continue to file the agreements as exhibits to its
Form 10-K.

    The Company is a biopharmaceutical company seeking to develop and
commercialize novel therapeutics based on RNA interference (“RNAi”). Patent
protection is critical to success in the research-based biotechnology
industry. Accordingly, license agreements are very much a part of the
ordinary course of business in the industry. As disclosed in its periodic
filings, including its Forms 10-K and 10-Q, part of the Company’s strategy is
to identify and acquire rights to patents and patent applications relevant to
the development of its RNAi therapeutic candidates. As part of this
strategy, the Company has entered into, and intends to continue to enter
into, agreements with respect to a broad portfolio of intellectual property
covering various aspects of RNAi technology. The license agreements with CRT,
Carnegie, Cold Spring and Stanford, pursuant to which the Company has
in-licensed rights to various aspects of RNAi technology, are part of this
ordinary course business strategy.

    In considering the materiality of license agreements for purposes of the
exhibit requirements under Item 601(b)(10) of Regulation S-K, the Company
considers the following factors:

    •

    The impact on the Company’s business (including the Company’s ability
to develop and commercialize RNAi therapeutics and the cost impact) in
the event the license was not available;

    •

    The applicability of the technology to the Company’s drug development
platform and/or drug development strategy;

    •

    The stage of development and value of the therapeutic(s) for which
the technology is relevant and the importance of such technology to the
development and commercialization of such therapeutics; and

    •

    The amount and timing of payments under the license agreement.

Securities and Exchange Commission

January 12, 2011

Page 3

    The Company acknowledges that its business continues to be substantially
dependent on licenses to certain fundamental patents applicable to all small
interfering RNAs (“siRNAs”) and to certain chemistry patents broadly
applicable to siRNAs, including its agreements with Max Planck discussed
below. However, due to the evolution of its patent portfolio and the scope of
the claims contained in certain patents and pending patent applications
covered by the CRT, Carnegie, Cold Spring and Stanford license agreements, as
well as the gradual transition of the Company’s patent portfolio to more
product focused intellectual property, the Company does not currently believe
its business is substantially dependent on these licenses, each of which
represents only a narrow aspect of the Company’s overall patent portfolio.

    The annual aggregate payments that the Company made to CRT, Carnegie, Cold
Spring and Stanford represented less than 1% of the Company’s total operating
expenses in each of 2009 and 2010. In addition, to the extent the Company is
required to make milestone or royalty payments under any of these agreements,
such payments will not represent a material percentage of its operating
expenses or cash, cash equivalents and marketable securities. Accordingly,
the Company does not believe that the payment of development or sales
milestone payments to any of CRT, Carnegie, Cold Spring or Stanford would be
material to the Company’s results of operations or financial condition.

    Notwithstanding the Company’s determination that the CRT, Carnegie, Cold
Spring and Stanford agreements are no longer material under Item 601(b)(10)
of Regulation S-K, the Company believes that disclosure of the patents and
patent applications licensed under the these agreements in its Form 10-K and
other filings provides meaningful information for investors regarding the
Company’s broad intellectual property portfolio.

    In response to the Staff’s comment regarding disclosure of the material terms
of the Max Planck agreements, including, but not limited to any payment
provisions, a range of royalty rates, aggregate milestones, usage
restrictions, exclusivity provisions and duration and termination provisions,
the Company intends to revise its disclosure regarding the Max Planck license
agreements in its Form 10-K for the year ended December 31, 2010 and to
continue to file these agreements as exhibits to its Form 10-K. The revised
disclosure will be substantially similar to that set forth below:

“In December 2002, we entered into a co-exclusive license with Max Planck Innovation (formerly
known as Garching Innovation GmbH) for the worldwide rights to use and sublicense certain patented
technology to develop and commercialize therapeutic products and related applications. We also
obtained the rights to use, without the right to sublicense, the technology for all diagnostic uses
other than for the purposes of therapeutic monitoring. In consideration for the rights to license
this technology, we issued to Max Planck Innovation 723,240 shares of Series B redeemable
convertible preferred stock with a fair value of $1.8 million. We were also given the right to
acquire

Securities and Exchange Commission

January 12, 2011

Page 4

the remaining 50 percent exclusive rights, which right we exercised upon our acquisition of
Ribopharma AG in July 2003. In consideration for the remaining rights to this technology, we
issued Max Planck Innovation an additional 158,605 shares of Series B redeemable convertible
preferred stock with a fair value of $0.4 million. The 881,845 shares of Series B redeemable
convertible preferred stock held by Max Planck Innovation converted into 464,128 shares of common
stock upon the closing of our initial public offering in June 2004.

In June 2005, we entered into an amendment to our agreement with Max Planck Innovation that secured
our exclusivity to use and sublicense certain patented technology to develop and commercialize
therapeutic products and related applications. In connection with this amendment, we issued
270,000 shares of our common stock, which were valued at $2.1 million, to Max Planck Innovation and
certain of its affiliated entities.

We are not obligated to pay any development or sales milestone payments to Max Planck Innovation,
however, we will be required to pay Max Planck Innovation future royalties on net sales of all
therapeutic and prophylactic products developed with the technology, if any.

Our agreements with Max Planck Innovation generally remain in effect until the expiration of the
last-to-expire patent licensed thereunder. We estimate that the principal issued patents covered
under the Max Planck Innovation agreements will expire both in and outside the United States during
2021, subject to any potential patent term extensions, restoration and/or supplemental protection
certificates extending such term extensions in countries where such extensions may become
available. We may terminate the agreements without cause with six months prior notice to Max
Planck Innovation, and Max Planck Innovation may terminate the agreements in the event that we
materially breach our obligations thereunder. Max Planck Innovation also has the right to
terminate the agreements in the event that we, independently or through a third party, attack the
validity of any of the licensed patents.”

Kyowa Hakko Kirin, page 20

    2.

    Please file as an exhibit in your 2010 Form 10-K, the license and collaboration agreement
with Kyowa Hakko Kirin dated June 2008. Alternatively, tell us the basis for your belief that
you are not required to file this agreement pursuant to Item 601(b)(10)(ii)(B) of Regulation
S-K.

              Response:

    As discussed in the Company’s response to Comment No. 1 above, the Company
analyzes each of its agreements for materiality when it enters into the agreement and
periodically thereafter. The Company has determined that its agreement with Kyowa
Hakko Kirin (“Kyowa Hakko”) is not a material contract required to be filed as an
exhibit under Item 601(b)(10) of Regulation S-K. Item 601(b)(10)(ii)(B) of Regulation
S-K clarifies that if an agreement is such as ordinarily accompanies the kind of
business conducted by the registrant, it will be deemed to be made in the ordinary
course of business, and therefore not required to be filed, unless the agreement is,
among other things, one “upon which the registrant’s business is substantially
dependent.” The Company has concluded that its agreement with Kyowa Hakko was made in

Securities and Exchange Commission

January 12, 2011

Page 5

    the ordinary course of the Company’s business and that its business is not
substantially dependent on the agreement, and accordingly, the Company has
not filed this agreement as an exhibit under Item 601(b)(10) of Regulation
S-K.

    The Company is a biopharmaceutical company seeking to develop and
commercialize novel therapeutics based on RNAi. As part of its collaboration
strategy, the Company seeks to enter into 50-50 co-development and/or
worldwide or specific geographic partnerships for specific RNAi therapeutic
programs in the ordinary course of business. Certain of these agreements may
be material to the Company due to a combination of various factors, including
the amount of any upfront payment, the amount of research and development
funding support, the potential future milestone and royalty revenue amounts,
and the geographic scope of the collaboration, among other factors. The Kyowa
Hakko agreement is a regional agreement that provides rights to Kyowa Hakko
to develop and commercialize the Company’s therapeutic candidate, ALN-RSV, at
its own expense in a limited geographic region. Under the Kyowa Hakko
agreement, there are modest development and sales milestone payments and
royalty rates, no co-development obligations, and no obligation on the part
of Kyowa Hakko to provide the Company with development assistance or specific
expertise outside of its limited geographic region.

    The Kyowa Hakko agreement does not fall within any of the enumerated
categories under Item 601(b)(10)(ii)(B) of Regulation S-K that would
disqualify it from the ordinary course exception. Notwithstanding the
Company’s determination that the Kyowa Hakko agreement is not material under
Item 601(b)(10) of Regulation S-K, the Company believes that disclosure of
this agreement in its Form 10-K and other filings provides meaningful
information for investors regarding the Company’s third-party collaboration
efforts.

Delivery Initiatives, page 24

    3.

    We note that during 2007, you obtained an exclusive worldwide license to the liposomal
delivery formulation technology of Tekmira for the discovery, development and
commercialization of LNP formulations for the delivery of RNAi therapeutics, and a
non-exclusive worldwide license to certain liposomal delivery of formulation technology of
Protiva Biotherapeutics Inc., for the discovery, development and commercialization of certain
LNP formulation for the delivery of RNAi therapeutics. Please provide the material terms of
each of these license agreements with Tekmira and Protiva, including, but not limited to any
payment provisions, a range of royalty rates, aggregate milestones, usage restrictions and
duration and termination provisions. Also, please file these agreements as exhibits in your
2010 Form 10-K, or alternatively, tell us the basis for your belief that you are not required
to file these agreements pursuant to Item 601(b)(10)(ii)(B) of Regulation S-K.

Securities and Exchange Commission

January 12, 2011

Page 6

              Response:

    The Company assesses the materiality of each contract it enters into upon signing
and will periodically reassess the materiality of each such agreement as its pipeline
matures and its business changes to determine whether it is reliant on any particular
service, technology or product, or whether any such agreement is otherwise required to
be filed as an exhibit pursuant to the requirements set forth in Item 601(b)(10) of
Regulation S-K. Given the advances of the Company’s clinical pipeline during 2010,
including the initiation of a second clinical development program utilizing the drug
delivery technology covered by the Tekmira and Protiva license agreements, the Company
determined that such agreements are now material to its business. Accordingly, in
response to the Staff’s comment regarding disclosure of the material terms of each of
the Tekmira and Protiva license agreements, including, but not limited to payment
provisions, royalty rates, aggregate milestone payments, usage restrictions and
duration and termination provisions, the Company intends to revise its disclosure
regarding the Tekmira and Protiva license agreements in its Form 10-K for the year
ended December 31, 2010 and to file these agreements as exhibits to its Form 10-K. The
revised disclosure will be substantially

CORRESP
1
filename1.htm

corresp

December 8, 2010

By EDGAR Submission

U.S. Securities and Exchange Commission

Division of Corporate Finance

100 F Street, N.E., Mail Stop 6010

Washington, D.C. 20549

Attention: Johnny Gharib

    Re:

    Alnylam Pharmaceuticals, Inc.

Form 10-K

Filed February 26, 2010

File No. 000-50743

Dear Mr. Gharib:

This letter relates to the letter, dated December 2, 2010 (the “Letter”), from Jeffrey Riedler of
the Staff of the U.S. Securities and Exchange Commission to John M. Maraganore, Chief Executive
Officer of Alnylam Pharmaceuticals, Inc. (the “Company”).

On behalf of the Company, and as discussed by telephone with you on December 7, 2010, this letter
confirms that the Company will respond to the Letter on or before January 13, 2011.

If you require additional information, please do not hesitate to contact me at 617-526-6443.

Sincerely,

    /s/ Clark W. Petschek

    Clark W. Petschek

    cc:

    Philip T. Chase, Esq.

Lia Der Marderosian, Esq.

December 2, 2010

John M. Maraganore, Ph.D. Chief Executive Officer Alnylam Pharmaceuticals, Inc. 300 Third Street
Cambridge, MA 02142

Re: Alnylam Pharmaceuticals, Inc.  Form 10-K
Filed February 26, 2010 File No. 000-50743
 Dear Mr. Maraganore:
 We have reviewed your filing and have the following comments.  In some of our
comments, we may ask you to provide us with  information so we may better understand your
disclosure.
 Please respond to this letter within te n business days by providing the requested
information, or by advising us when you will provide the requested response.  If you do not believe our comments apply to your facts and circum stances, please tell us w hy in your response.
 After reviewing the information you provide in response to these comments, we may
have additional comments.
Form 10-K, filed February 26, 2010

Business, page 2

1. We note that you have included as exhibits various license agreements with each of
Cancer Research Technology Limited, Carneg ie Institution of Washington, Cold Spring
Harbor Laboratory, Garching Innovation Gm bH (now known as Max Planck Innovation
GmbH) and The Board of Trustees of the Le land Stanford Junior University.  Please
describe the material terms of each of thes e agreements, including, but not limited to any
payment provisions, a range of royalty rates,  aggregate milestones,  usage restrictions,
exclusivity provisions and durati on and termination provisions.

Kyowa Hakko Kirin, page 20

2. Please file as an exhibit in your 2010 Form 10-K, the license and collaboration agreement
with Kyowa Hakko Kirin dated June 2008. Alterna tively, tell us the basis for your belief
that you are not required to file this agreement pursuant to Item 601(b)(10)(ii)(B) of

John M. Maraganore, Ph.D. Alnylam Pharmaceuticals, Inc.
December 2, 2010 Page 2

Regulation S-K.
Delivery Initiatives, page 24

3. We note that during 2007, you obtained an excl usive worldwide license to the liposomal
delivery formulation technology of Tekmir a for the discovery, development and
commercialization of LNP formulations for th e delivery of RNAi therapeutics, and a non-
exclusive worldwide license to certain liposomal delivery formulation technology of
Protiva Biotherapeutics Inc., for the discove ry, development and commercialization of
certain LNP formulation for the delivery of RNAi therapeutics.  Please provide the material terms of each of these license agre ements with Tekmira and Protiva, including,
but not limited to any payment provisions, a ra nge of royalty rates, aggregate milestones,
usage restrictions and duration and termina tion provisions.  Also, please file these
agreements as exhibits in your 2010 Form 10-K,  or alternativ ely, tell us the basis for your
belief that you are not required to file these agreements pursuant to Item 601(b)(10)(ii)(B) of Regulation S-K.
 Manufacturing, page 39

4. We note that in 2009, you entered into a ma nufacturing and supply agreement with
Tekmira where you are committed to pay Tekmira a minimum of CAD $11.2 million
(representing U.S. $9.2 million at the tim e of execution) through December 2011 for
manufacturing services.  Please file the agr eement as an exhibit in your 2010 Form 10-K,
or alternatively, tell us  the basis for your belief that you are not required  to file the
agreement pursuant to Item 601(b )(10)(ii)(B) of Regulation S-K.

Proxy Statement on Schedule 14A, filed April 20, 2010

2009 Annual Incentive Program, page 26

5. We note that your annual cash incentive award is based on the achievement of corporate
goals and individual objectives.  However, your disc ussion does not disclose the
corporate goals used as part of the determination of annual cash incentive awards.  In addition, while your discussion does disclose individual objectives , it does not quantify
any targeted levels of achievement or actual levels of achievement, where these objectives are quantitative.  Please provide draft disclosure for your 2011 proxy statement which provides your 2010 corporate goals a nd individual objectives  as well as the
targeted levels of achievement.  To the extent that the goals and objectives are quantitative, the discussion of goals and achievements should also be quantitative.  Please also confirm that in your 2011 proxy statement you will discuss the levels of achievement
of the goals and objectives for each Named Executive Officer.

John M. Maraganore, Ph.D. Alnylam Pharmaceuticals, Inc. December 2, 2010 Page 3

Form 10-Q for the Quarterly Period Ended September 30, 2010

Strategic Alliances, page 23

6. We note that in November 2010, you formed a collaboration with Medtronic and CHDI
to advance ALN-HTT.  We also note that in the United States, you have the opportunity
to invest in clinical development through pr oduct launch in return for a proportional share
of the profits, and in Europe, Medtronic is solely responsible for development and
commercialization, and you are eligible to receive milestones and royalties on product
sales, if any.  Please describe the materi al terms of the collaboration agreement,
including, but not limited to the material obl igations and rights of each party to the
agreement, the payment provisions, a range of royalty rates, a ggregate milestones and
duration and termination provision s.  Also, please file the agre ement as an exhibit in your
2010 Form 10-K, or alternatively, tell us the basis for your belief that you are not
required to file the agreement pursuant to Item 601(b)(10)(ii)(B ) of Regulation S-K.

We urge all persons who are responsible for th e accuracy and adequacy of the disclosure
in the filing to be certain that the filing include s the information the Securities Exchange Act of
1934 and all applicable Exchange Act rules requir e.  Since the company and its management are
in possession of all facts relating to a company’s disclosure, they are responsible for the accuracy
and adequacy of the disclosures they have made.
 In responding to our comments, please provi de a written statement from the company
acknowledging that:
• the company is responsible for the adequacy and accuracy of the disclo sure in the filing;

• staff comments or changes to disclosure in response to staff comments do not foreclose
the Commission from taking any action with respect to the filing; and

• the company may not assert staff comments as a defense in any proceeding initiated by
the Commission or any person under the federa l securities laws of  the United States.

You may contact Johnny Gharib  at (202) 551-3170 or me at  (202) 551-3715 if you have
any questions.

Sincerely,
       Jeffrey Riedler
Assistant Director

Via Facsimile and U.S. Mail Mail Stop 6010
March 2, 2009
         Dr. John M. Maraganore Chief Executive Officer Alnylam Pharmaceuticals, Inc. 300 Third Street Cambridge, MA 02142
Re: Alnylam Pharmaceuticals, Inc.
 Form 10-K for the Fiscal Year Ended December 31, 2007  File No. 000-50743

Dear Dr. Maraganore:   We have completed our review of your Form 10-K and have no further comments
at this time.
       S i n c e r e l y ,
         C a r l t o n  T a r t a r         B r a n c h  C h i e f

CORRESP
1
filename1.htm

corresp

February 24, 2009

By EDGAR Transmission

Securities and Exchange Commission

Division of Corporate Finance

100 F Street, N.E., Mail Stop 6010

Washington, D.C. 20549

Attention: Christine Allen

    Re:

    Alnylam Pharmaceuticals, Inc.

Form 10-K for the Fiscal Year Ended December 31, 2007

File No. 000-50743

Ladies and Gentlemen:

On behalf of Alnylam Pharmaceuticals, Inc. (the “Company”), I am writing in response to comments
contained in the letter dated February 20, 2009 (the “Letter”) from Jim B. Rosenberg of the Staff
(the “Staff”) of the Securities and Exchange Commission (the “Commission”) to John M. Maraganore,
the Company’s Chief Executive Officer. The responses set forth below are keyed to the numbering of
the comments and the headings used in the Letter.

Intellectual Property Related to Fundamental Aspects and Uses of siRNA and RNAi related
Mechanisms, page 18

    1.

    In response to our previous comment 3, you state that you will include the expiration dates
of patents material to your business in future filings. Please respond with the disclosure
relating to these patents that you propose to include in future filings.

    Response:

    In response to previous comment 3, the Company intends to include a revised table,
including a column with expiration dates, and revised disclosure substantially similar
to that set forth below in its Form 10-K for the year ended December 31, 2008:

“Intellectual Property Related to Fundamental Aspects and Uses of siRNA and RNAi-related Mechanisms

In this category, we include United States and foreign patents and patent applications that claim
key aspects of siRNA architecture and RNAi-related mechanisms. Specifically included are patents
and patent applications covering targeted cleavage of mRNA directed by RNA-like oligonucleotides,
double-stranded RNAs of particular lengths and particular structural features,

Securities and Exchange Commission

February 24, 2009

Page 2

such as blunt and/or overhanging ends. Our strategy has been to secure exclusive rights where
possible and appropriate to key patents and patent applications we believe cover fundamental
aspects of RNAi. The following table lists patents and/or patent applications to which we have
secured rights that we regard as being fundamental for the use of siRNAs as therapeutics.

    Licensor/Patent

    First Priority

    Status

    Owner

    Subject Matter

    Date

    Inventors

    Patent Number

    Expiration Date*

    Alnylam Rights

    Isis

    Inactivation of
target mRNA

    6/6/1996 and
6/6/1997

    S. Crooke

    U.S. 5,898,031,
U.S. 6,107,094 &
U.S. 7,432,250

    06/06/2016

    Exclusive rights
for therapeutic
purposes related to
siRNAs**

    EP 0928290

    06/06/2017

    Additional applications pending in the
U.S. and several foreign jurisdictions

    Carnegie
Institution of
Washington

    Double-stranded
RNAs to induce RNAi

    12/23/1997

    A. Fire,
C. Mello

    U.S. 6,506,559

    12/18/2018

    Non-exclusive

rights for

therapeutic

purposes

    Additional applications pending in the
U.S. and several foreign jurisdictions

    Medical College of
Georgia Research
Institute, Inc.

    Methods for

inhibiting gene

expression using

double-stranded RNA

    1/28/1999

    Y. Li, M, Farrell,
M. Kirby

    AU 776150

(Australia)

    1/28/2020

    Exclusive rights

    Additional applications pending in the
U.S., Europe and Canada

    Alnylam

    Small double-

stranded RNAs as therapeutic

products

    1/30/1999

    R. Kreutzer, S.
Limmer

    EP 1214945

(revoked/to be

appealed) & EP

1550719,

CA 2359180

(Canada),

AU 778474

(Australia),

ZA 2001/5909 (South Africa)

DE 20023125 U1, DE

10066235 & DE

10080167 (Germany)

    01/29/2020

    Owned

    Additional applications pending in the
U.S. and several foreign jurisdictions

    Alnylam

    Composition and
methods for
inhibiting a target
nucleic acid with
double-stranded RNA

    4/21/1999

    C. Pachuk, C.
Satishchandran

    AU 781598

(Australia)

    4/19/2020

    Owned

    Additional applications pending in the
U.S. and many other additional countries
worldwide

    Cancer Research
Technology Limited

    RNAi uses in
mammalian oocytes,
preimplantation
embryos and somatic
cells

    11/19/1999

    M. Zernicka-Goetz,
M.J. Evans, D.M.
Glover

    EP 1230375

(revoked/to be

appealed), SG 89569

(Singapore),

AU 774285

(Australia)

    11/17/2020

    Exclusive rights

for therapeutic

purposes

    Additional applications pending in the
U.S. and several foreign jurisdictions

Securities and Exchange Commission

February 24, 2009

Page 3

    Licensor/Patent

    First Priority

    Status

    Owner

    Subject Matter

    Date

    Inventors

    Patent Number

    Expiration Date*

    Alnylam Rights

    Massachusetts
Institute of
Technology,
Whitehead
Institute, Max
Planck
Gesellschaft***

    Mediation of RNAi
by small RNAs 21-23
base pairs long

    3/30/2000

    D.P. Bartel, P.A.
Sharp, T. Tuschl,
P.D. Zamore

    AU 2001249622

(Australia)

    03/30/2020

    Non-exclusive

rights for

therapeutic

purposes***

    Additional applications pending in the
U.S. and many other additional countries
worldwide

    Max Planck

Gesellschaft

    Synthetic and
chemically modified
siRNAs as
therapeutic
products

    12/01/2000,
04/24/2004 and
04/27/2004

    T. Tuschl, S.
Elbashir, W.
Lendeckel

    U.S. 7,056,704 &
U.S. 7,078,196,
EP 1407044,
AU 2002235744
(Australia),
ZA 2003/3929 (South
Africa), SG 96891
(Singapore),
NZ 52588 (New
Zealand),
JP 4 095 895,
RU 2322500 (Russia)

    11/29/2021

    Exclusive rights

for therapeutic

purposes

    Additional applications pending in the
U.S. and many other countries worldwide

    Alnylam

    Methods for
inhibiting a target
nucleic acid via
the introduction of
a vector encoding a
double-stranded RNA

    1/31/2001

    T. Giordano, C.
Pachuk, C.
Satishchandran

    AU 785395

(Australia)

    1/31/2021

    Owned

    Additional applications pending in the
U.S., Australia and Canada

    Cold Spring Harbor

Laboratory

    RNAi uses in

mammalian cells

    3/16/2001

    D. Beach, G. Hannon

    Pending in the U.S. and  many countries
worldwide

    Non-exclusive

rights for

therapeutic

purposes

    Stanford University

    RNAi uses in vivo in mammalian liver

    7/23/2001

    M.A. Kay, A.P.
McCaffrey

    AU 2002326410

(Australia)

    7/23/2021

    Exclusive rights

for therapeutic

purposes

    Additional applications pending in the
U.S. and many other countries worldwide

    *

    For applications filed after June 7, 1995, the patent term generally
is 20 years from the earliest application filing date. However, under
the Drug Price Competition and Patent Term Extension Act of 1984,
known as the Hatch-Waxman Act, we may be able to apply for patent term
extensions for our U.S. patents. We cannot predict whether or not any
patent term extensions will be granted or the length of any patent
term extension that might be granted.

    **

    We hold co-exclusive therapeutic rights with Isis. However, Isis has
agreed not to license such rights to any third party, except in the
context of a collaboration in which Isis plays an active role.

    ***

    We hold exclusive rights to the interest owned by three co-owners. A
separate entity, the University of Massachusetts, has licensed its
purported interest separately to third parties.

Intellectual Property Related to Chemical Modifications

Our collaboration and license agreement with Isis provides us with rights to practice the
inventions covered by over 200 issued patents worldwide, as well as rights based on future
chemistry patent applications through March 2009. These patents will expire both in and outside the
United States generally between 2009 and 2029, subject to any potential patent term

Securities and Exchange Commission

February 24, 2009

Page 4

extensions and/or supplemental protection certificates extending such term extensions in countries
where such extensions may become available. These inventions cover chemical modifications we may
wish to incorporate into our RNAi therapeutic products. Under the terms of our license agreement,
Isis agreed not to grant licenses under these patents to any other organization for dsRNA products
designed to work through an RNAi mechanism, except in the context of a collaboration in which Isis
plays an active role.

Intellectual Property Related to siRNAs Directed to Specific Targets

We have filed a number of patent applications claiming specific siRNAs directed to various gene
targets that correlate to specific diseases. While there may be a significant number of competing
applications filed by other organizations claiming siRNAs to treat the same gene target, we were
among the first companies to focus and file on RNAi therapeutics, and thus, we believe that a
number of our patent applications may predate competing applications that others may have filed.
Reflecting this, in August 2005, the EPO granted a broad patent, which we call the Kreutzer-Limmer
II patent, with 103 allowed claims on therapeutic compositions, methods and uses comprising siRNAs
that are complementary to mRNA sequences in over 125 disease target genes. The Kreutzer-Limmer II
patent will expire on January 9, 2022, subject to any potential patent term extensions and/or
supplemental protection certificates extending such term extensions in countries where such
extensions may become available. Some of these claimed gene targets are being pursued by our
development and pre-clinical programs, such as those expressed by viral pathogens including RSV and
influenza virus. In addition, the claimed targets include oncogenes, cytokines, cell adhesion
receptors, angiogenesis targets, apoptosis and cell cycle targets, and additional viral disease
targets, such as hepatitis C virus and HIV. The Kreutzer-Limmer II patent series is pending in the
United States and many foreign countries.”

Material Agreements

    2.

    We note your response that you analyzed each agreement for materiality and that you
determined that the agreements are not material, and thus do not need to be filed as exhibits
as required by Item 601(b)(10) of Regulation S-K. Please provide us a comprehensive analysis,
including any relevant facts and circumstances you considered, that led to your conclusions
that these agreements are not material.

    Response:
    Item 601(b)(10)(ii)(B) of Regulation S-K clarifies that if an agreement is such as
ordinarily accompanies the kind of business conducted by the registrant, it will be
deemed to be made in the ordinary course of business, and therefore not required to be
filed, unless the agreement is, among other things, one “upon which the registrant’s
business is substantially dependent.”

    The Company has concluded that its license agreements with Tekmira
Pharmaceuticals Corporation (“Tekmira”) and the Massachusetts Institute of
Technology (“MIT”) were made in the ordinary course of the

Securities and Exchange Commission

February 24, 2009

Page 5

    Company’s business and that its business is not substantially dependent on
either agreement.

    Patent protection is critical to success in the research-based biotechnology
industry. Accordingly, license agreements are very much a part of the
ordinary course of business in the industry. In addition, as disclosed in
its periodic filings, including Forms 10-K and 10-Q, part of the Company’s
strategy is to identify and acquire rights to drug delivery technology for
its RNAi therapeutic candidates. As part of this strategy, the Company has
entered into, and intends to continue to enter into, agreements with respect
to delivery technology. The license agreements with Tekmira and MIT,
pursuant to which the Company has in-licensed delivery technology, are part
of this ordinary course business strategy.

    In considering the materiality of license agreements for purposes of the
exhibit requirements under Item 601(b)(10)(ii)(B), the Company considers the
following factors:

    •

    The impact to the Company’s business (including the freedom to
develop and commercialize RNAi therapeutics and the cost impact) in the
event the license was not available;

    •

    The applicability of the technology to the Company’s drug
development platform and/or drug development strategy;

    •

    The stage of development and value of the therapeutic(s) for which
the technology is relevant and the importance of such technology to the
successful development and commercialization of such therapeutics; and

    •

    The amount and timing of payments under the license agreement.

    By definition, the exhibit requirements under Item 601(b)(10)(ii)(B) do not
apply to licenses upon which the Company’s business is not substantially
dependent. The Company acknowledges that its business is substantially
dependent on licenses to fundamental patents applicable to all siRNAs and to
certain chemistry patents broadly applicable to siRNAs. However, the Company
does not currently believe its business is substantially dependent on
licenses to technology, such as the delivery technology in-licensed from
Tekmira and MIT, that is not broadly applicable to siRNAs.

    The Company believes it will likely be required to employ a different
delivery technology for each RNAi therapeutic candidate that it develops.
For example, while the Company is currently using the liposomal delivery
technology licensed under the Tekmira agreement in its Phase I ALN-VSP
product candidate, it will not use such technology with its lead product,

Securities and Exchange Commission

February 24, 2009

Page 6

    ALN-RSV. Furthermore, the Company does not yet know whether it will
successfully develop any therapies incorporating the technology licensed
under the Tekmira or MIT license agreement. Examples of other drug delivery
technologies that the Company will likely consider utilizing include (i)
polymers, (ii) cholesterol conjugates, (iii) carbohydrate conjugates, (iv)
antibodies and (v) peptides or other proteins.

    The annual payments that the Company made to each of Tekmira and MIT
represented less than 2% of the Company’s total operating expenses in 2007
and 2008. Until the Company is required to pay milestones or royalties, as
described below, its annual payment obligations under the agreements will
not increase.

    Under the Tekmira agreement, the Company will be required to make
development milestone payments totaling up to $10.0 million, sales milestone
payments totaling up to $6.0 million and royalty payments on sales, if any,
of products using the licensed technology. Under the MIT agreement, the
Company will be required to make development milestone payments totaling up
to $1.25 million and to pay royalties on sales, if any, of products using
the licensed technology. The Company expects that, if and when it is
required to make milestone or royalty payments under either the Tekmira or
MIT agreement, such payments will not represent a material percentage of its
operating expenses or cash, cash equivalents and marketable securities.
Accordingly, the Company does not believe that the payment of development or
sales milestones will be material to its results of operations or financial
condition, especially when considering that the payment of development
milestones would indicate positive developments that could lead to
additional revenue.

    The Company expects to explore numerous delivery technologies as it builds
its product pipeline and as drug delivery technologies evolve and also
expects to continue to enter into drug delivery license agreements in the
ordinary course of its business. The Company believes it is unlikely that
any such technology will be broadly applicable to RNAi therapeutics and,
therefore, does not currently anticipate that its business will be
substantially depend

CORRESP
1
filename1.htm

corresp

January 22, 2009

By EDGAR Transmission

Securities and Exchange Commission

Division of Corporate Finance

100 F Street, N.E., Mail Stop 6010

Washington, D.C. 20549

Attention: Christine Allen

    Re:

     Alnylam Pharmaceuticals, Inc.

Form 10-K for the Fiscal Year Ended December 31, 2007

File No. 000-50743

Ladies and Gentlemen:

On behalf of Alnylam Pharmaceuticals, Inc. (the “Company”), I am writing in response to comments
contained in the letter dated December 9, 2008 (the “Letter”) from Jim B. Rosenberg of the Staff
(the “Staff”) of the Securities and Exchange Commission (the “Commission”). The responses set
forth below are keyed to the numbering of the comments and the headings used in the Letter.

Material Agreements

    1.

    We note that you refer to several agreements throughout your Form 10-K and proxy statement,
most notably the agreements with Tekmira Pharmaceuticals Corporation and the Massachusetts
Institute of Technology. It appears that these agreements may be material to your business,
but they are not filed as exhibits to your Form 10-K. Please explain why you do not believe
that these agreements are material to your business, or, alternatively, please file them as
exhibits to your 10-K.

    Response:

    The Company analyzes each of its agreements for materiality when it enters into
the agreement. With respect to the Company’s agreements with Tekmira Pharmaceuticals
Corporation (“Tekmira”) and Massachusetts Institute of Technology (“MIT”), the Company
has determined that neither agreement is a material contract required to be filed as an
exhibit under Regulation S-K Item 601(b)(10). The Company is actively working to
extend its capabilities to advance the development and commercialization of its product
candidates. As part of this business plan and as a means of obtaining resources and
funding, the Company enters into technology license and collaboration agreements, such
as the Tekmira and MIT agreements, in the ordinary course of business. Neither the
Tekmira nor the MIT contract falls within any of the enumerated categories under Item
601(b)(10)(ii) that would disqualify them from the ordinary course exception.
Notwithstanding the Company’s determination that the Tekmira and MIT agreements are not
material under Item 601(b)(10), the Company believes that disclosure of these
agreements in

300 Third Street • Cambridge MA, 02142 • main 617.551.8200 • fax 617.551.8101 •
www.alnylam.com

Securities and Exchange Commission

January 22, 2009

Page 2

    its Form 10-K and other filings provides meaningful information for investors
regarding the Company’s third-party collaboration efforts.

Strategic Alliances, page 13

    2.

    Please revise your disclosure in this section to include the following material terms:

    Roche, pages 13-14

    •

    the other therapeutic areas that Roche may expand the license to and the amount
of additional payments they may receive to do so

    •

    the aggregate development and sales milestone payments

    •

    the expiration date of the last-to-expire patent covered under the license
agreement

    Novartis, pages 14-15

    •

    aggregate potential research payments and milestone payments

    •

    additional payments to be made by Novartis upon exercise of the integration
option

    •

    explanation of the operation of the integration option

    •

    funding commitments from Novartis for pandemic flu alliance

    Biogen Idec, page 16

    •

    aggregate milestone payments

    •

    duration and expiration of the agreement

    Isis, page 16

    •

    aggregate developmental and regulatory milestone payments and license fee

    •

    duration and expiration of the agreement

    Response: Roche

    •

    In response to the Staff’s comment regarding the other therapeutic
areas that Roche may expand the license to and the amount of additional payments
associated with doing so, the Company intends to revise its disclosure regarding
the Roche license and collaboration agreement in its Form 10-K for the year ended
December 31, 2008. Such revised disclosure will be substantially similar to that
set forth below:

“In July 2007, we and, for limited purposes, Alnylam Europe AG, or Alnylam Europe, entered into a
license and collaboration agreement with Roche. Under the license and collaboration agreement,
which became effective in August 2007, we granted Roche a non-exclusive license to our intellectual
property to develop and commercialize therapeutic products that function through RNAi, subject to
our existing contractual obligations to third parties. The license is initially limited to the
therapeutic areas of oncology, respiratory diseases, metabolic diseases and certain liver diseases,
and may be expanded to include up to 18 additional therapeutic areas, comprising all other fields
of human disease, as identified and agreed upon by the parties, upon payment to us by Roche of an
additional $50.0 million for each additional therapeutic area, if any.”

Securities and Exchange Commission

January 22, 2009

Page 3

    •

    In response to the Staff’s comment regarding the aggregate development
and sales milestone payments, the Company intends to revise its disclosure
regarding the Roche license and collaboration agreement in its Form 10-K for the
year ended December 31, 2008. Such revised disclosure will be substantially
similar to that set forth below:

“In consideration for the rights granted to Roche under the license and collaboration agreement,
Roche paid us $273.5 million in upfront cash payments. In addition, in exchange for our
contributions under the collaboration agreement, for each RNAi therapeutic product successfully
developed by Roche, its affiliates or sublicensees under the collaboration agreement, if any, we
are entitled to receive milestone payments upon achievement of specified development and sales
events, totaling up to an aggregate of $100.0 million per therapeutic target, together with royalty
payments based on worldwide annual net sales, if any. Due to the uncertainty of pharmaceutical
development and the high historical failure rates associated with drug development, we may not
receive any milestone or royalty payments from Roche.”

    •

    In response to the Staff’s comment regarding the expiration date of the
last-to-expire patent covered under the Roche license and collaboration agreement,
the Company intends to revise its disclosure regarding such agreement in its Form
10-K for the year ended December 31, 2008. Such revised disclosure will be
substantially similar to that set forth below:

“The term of the license and collaboration agreement generally ends upon the later of ten years
from the first commercial sale of a licensed product and the expiration of the last-to-expire
patent covering a licensed product. We estimate that our principal issued patents covered under
the license and collaboration agreement will expire both in and outside the United States generally
between 2016 and 2025, subject to any potential patent term extensions and/or supplemental
protection certificates extending such term extensions in countries where such extensions may
become available.”

    Novartis

    •

    In response to the Staff’s comment regarding the aggregate potential
research payments and milestone payments, the Company intends to revise its
disclosure regarding the Novartis collaboration and license agreement in its Form
10-K for the year ended December 31, 2008. Such revised disclosure will be
substantially similar to that set forth below:

“The collaboration and license agreement includes terms under which Novartis will provide us with
research funding and development and sales milestone payments as well as royalties on annual net
sales of products resulting from the collaboration, if any. The amount of research funding provided by
Novartis under the collaboration and license agreement during the research term is dependent upon
the number of active programs that we are collaborating with them on at any given time and the
number of our employees that are working on those programs, in respect of which Novartis

Securities and Exchange Commission

January 22, 2009

Page 4

reimburses us at an agreed upon rate. Under the terms of the collaboration and license
agreement, Novartis has the right to select up to 30 exclusive targets to include in the
collaboration, which number may be increased to 40 under certain circumstances. For RNAi
therapeutic products successfully developed under the agreement, if any, we would be entitled to
receive milestone payments upon achievement of certain specified development and annual net sales
events, up to an aggregate of $75.0 million per therapeutic target. Due to the uncertainty of
pharmaceutical development and the high historical failure rates associated with drug development,
we may not receive any milestone or royalty payments from Novartis.

Under the terms of the collaboration and license agreement, we retain the right to discover,
develop, commercialize or manufacture compounds that function through the mechanism of RNAi, or
products that contain such compounds as an active ingredient, with respect to targets not selected
by Novartis for inclusion in the collaboration, provided that Novartis has a right of first offer
with respect to an exclusive license for additional targets before we partner any of those
additional targets with third parties.”

    •

    In response to the Staff’s comment regarding additional payments to be
made by Novartis upon exercise of the integration option, the Company intends to
revise its disclosure regarding the Novartis collaboration and license agreement in
its Form 10-K for the year ended December 31, 2008. Such revised disclosure will
be substantially similar to that set forth below:

“In connection with the exercise of the integration option, Novartis would be required to make
additional payments to us totaling $100.0 million, which payments would include an option exercise
fee, a milestone based on the overall success of the collaboration and pre-paid milestones and
royalties which could become due as a result of future development of products using our
technology.”

    •

    In response to the Staff’s comment regarding operation of the
integration option, the Company intends to revise its disclosure regarding the
Novartis collaboration and license agreement in its Form 10-K for the year ended
December 31, 2008. Such revised disclosure will be substantially similar to that
set forth below:

“The collaboration and license agreement also provides Novartis with a non-exclusive option to
integrate into its operations our intellectual property relating to RNAi technology, excluding any
technology related to delivery of nucleic acid based molecules. Novartis may exercise this
integration option at any point during the research term, as defined in the collaboration and
license agreement. The research term expires in October 2009 and may be extended until October
2010 at Novartis’ election. In connection with the exercise of the integration option, Novartis
would be required to make additional payments to us totaling $100.0 million, which payments would
include an option exercise fee, a milestone based on the overall success of the collaboration and pre-paid
milestones and royalties which could become due as a result of future development of products using
our technology. The license grant under the integration option, if exercised by Novartis, would be structured
similarly to our non-exclusive platform licenses with Roche and Takeda.”

Securities and Exchange Commission

January 22, 2009

Page 5

    •

    In response to the Staff’s comment regarding funding commitments from
Novartis for the pandemic flu alliance, the Company intends to revise its
disclosure regarding the Novartis collaboration and license agreement in its Form
10-K for the year ended December 31, 2008. Such revised disclosure will be
substantially similar to that set forth below:

“In February 2006, we entered into the Novartis flu alliance. Under the terms of the Novartis flu
alliance, we and Novartis have joint responsibility for the development of RNAi therapeutics for
pandemic flu. This program was stopped and currently there are no specific resource commitments for
this program.”

    Biogen Idec

    •

    In response to the Staff’s comment regarding the aggregate milestone
payments under the Biogen Idec license and collaboration agreement, the Company
intends to revise its disclosure regarding the agreement in its Form 10-K for the
year ended December 31, 2008. Such revised disclosure will be substantially
similar to that set forth below:

“We received an upfront $5.0 million payment from Biogen Idec. In addition, upon the successful
development and utilization of a product resulting from the collaboration, if any, Biogen Idec
would be required to pay us milestone payments, totaling $51.0 million, and royalty payments on
sales, if any. Due to the uncertainty of pharmaceutical development and the high historical
failure rates associated with drug development, we may not receive any milestone or royalty
payments from Biogen Idec.”

    •

    In response to the Staff’s comment regarding the duration and
expiration of the Biogen Idec license and collaboration agreement, the Company
intends to revise its disclosure regarding the agreement in its Form 10-K for the
year ended December 31, 2008. Such revised disclosure will be substantially
similar to that set forth below:

“Unless earlier terminated, the collaboration and license agreement will remain in effect until the
expiration of all payment obligations under the agreement. Either we or Biogen Idec may terminate
the agreement in the event that the other party breaches its obligations thereunder. Biogen Idec
may also terminate the agreement, on a country-by-country basis, without cause upon 90 days prior
notice.”

    Isis

    •

    In response to the Staff’s comment regarding aggregate developmental
and regulatory milestone payments and license fee, the Company intends to revise
its disclosure regarding the Isis collaboration and license agreement in its

Securities and Exchange Commission

January 22, 2009

Page 6

    Form 10-K for the year ended December 31, 2008. Such revised disclosure
will be substantially similar to that set forth below:

“Under the terms of the Isis agreement, we paid Isis an upfront license fee of $5.0 million. We
also agreed to pay Isis milestone payments, totaling up to approximately $3.4 million, upon the
occurrence of specified development and regulatory events, and royalties on sales, if any, for each
product that we or a collaborator develops using Isis intellectual property.

Isis has agreed to pay us, per therapeutic target, a license fee of $0.5 million, and milestone
payments totaling approximately $3.4 million, payable upon the occurrence of specified development
and regulatory events, and royalties on sales, if any, for each product developed by Isis or a
collaborator that utilizes our intellectual property. Isis initially had the right to elect up to
ten non-exclusive target licenses under the agreement and has the right to purchase one additional
non-exclusive target per year during the term of the collaboration. Due to the uncertainty of
pharmaceutical development and the high historical failure rates associated with drug development,
we may not receive any milestone or royalty payments from Isis or be required to make any milestone
or royalty payments to Isis.”

    •

    In response to the Staff’s comment regarding the duration and
expiration of the Isis collaboration and license agreement, the Company intends to
revise its disclosure regarding the agreement in its Form 10-K for the year ended
December 31, 2008. Such revised disclosure will be substantially similar to that
set forth below:

“The term of

CORRESP
1
filename1.htm

corresp

    Clark W. Petschek

    December 17, 2008

    +1 617 526 6443 (t)

+1 617 526 5000 (f)

    By EDGAR Submission

    clark.petschek@wilmerhale.com

Securities and Exchange Commission

Division of Corporate Finance

100 F Street, N.E., Mail Stop 6010

Washington, D.C. 20549

Attention: Christine Allen

    Re:

    Alnylam Pharmaceuticals, Inc.

Form 10-K for the Fiscal Year Ended December 31, 2007

File No. 000-50743

Dear Ms. Allen:

Pursuant to our telephone conversation today, I am confirming Alnylam Pharmaceuticals, Inc.’s
request for, and your acceptance of, an extension of time to respond to the comments of the Staff
of the Securities and Exchange Commission in the above referenced matter. As discussed, Alnylam
intends to submit its response not later than January 22, 2009.

Thank you for your consideration in this matter and please feel free to call me at the above number
if you have any questions.

Sincerely,

/s/ Clark W. Petschek

Clark W. Petschek

    cc:

    Philip T. Chase, Esq.

Lia Der Marderosian, Esq.

Wilmer Cutler Pickering Hale and Dorr llp, 60  State Street, Boston, Massachusetts 02109

Beijing    Berlin    Boston    Brussels    Frankfurt    London     Los Angeles    New York     Oxford    Palo Alto    Waltham    Washington

Via Facsimile and U.S. Mail Mail Stop 6010
December 9, 2008
         Ms. Patricia Allen Vice President of Finance and Treasurer Alnylam Pharmaceuticals, Inc. 300 Third Street Cambridge, MA  02142
Re: Alnylam Pharmaceuticals, Inc.
 Form 10-K for the Fiscal Year Ended December 31, 2007  File No. 000-50743

Dear Ms. Allen:
We have reviewed your filing and have the following comments.  In our
comments, we ask you to provide us with  information to better understand your
disclosure.  Where a comment requests you to  revise disclosure, the information you
provide should show us what the revised disc losure will look like and identify the annual
or quarterly filing, as appli cable, in which you intend to fi rst include it.  If you do not
believe that revised disclosure  is necessary, explain the reason in your response.  After
reviewing the information provided, we may raise additional comments and/or request
that you amend your filing.

 Please understand that the purpose of our re view process is to assist you in your
compliance with the applicable disclosure  requirements and to  enhance the overall
disclosure in your filing.  We look forward to  working with you in these respects.  We
welcome any questions you may have about our  comments or on any other aspect of our
review.  Feel free to call us at the telephone numbers listed at the end of this letter.
 Material Agreements

1. We note that you refer to several ag reements throughout your Form 10-K and
proxy statement, most notably the agr eements with Tekmira Pharmaceuticals
Corporation and the Massachusetts Institute  of Technology.  It appears that these
agreements may be material to your business,  but they are not f iled as exhibits to
your Form 10-K.  Please explain why you do not believe that these agreements
are material to your business, or, alternativ ely, please file them as exhibits to your
10-K.

Ms. Patricia Allen
Alnylam Pharmaceuticals, Inc.  December 9, 2008 Page 2
 Strategic Alliances, page 13

2. Please revise your disclosure in this s ection to include the following material
terms:
Roche, pages 13-14
• the other therapeutic areas that Roche may expand the license to and the
amount of additional payments they may receive to do so
• the aggregate development and sales milestone payments
• the expiration date of the last-to-e xpire patent covered under the license
agreement
Novartis, pages 14-15
• aggregate potential research payments and milestone payments
• additional payments to be made by Novartis upon exercise of the
integration option
• explanation of the operation of the integration option
• funding commitments from Novartis for pandemic flu alliance
Biogen Idec, page 16
• aggregate milestone payments
• duration and expiration of the agreement
Isis, page 16
• aggregate developmental and regulator y milestone payments and license
fee
• duration and expiration of the agreement

Intellectual Property Related to Fundamental Aspects and Uses of siRNA and RNAi-
related Mechanisms, page 18
3. Please revise the table in this section to include disclosure of the expiration dates
of the various patents.

Note 11. Significant Agreements
Roche Alliance, page 99
4. Your disclosure states “As future milest ones are achieved, and to the extent they
are within the five year term, the am ounts will be recogn ized as revenue
prospectively over the remaining period of  performance.”  Please revise your
disclosure a) to specify whether and to what extent you recogni ze a portion of the
milestone when achieved including your method for determining the amount recognized and b) to what extent and how you recognize any remaining portion of
the achieved milestone “prospectively over th e remaining period of performance.”
Further, specify the accounting, if different, for the milestones under the other agreements where future milest one payments may be received.

Ms. Patricia Allen
Alnylam Pharmaceuticals, Inc.  December 9, 2008 Page 3
 *    *    *    *

Please respond to these comments within  10 business days or tell us when you
will provide us with a response.   Your letter should key your responses to our comments.
Detailed cover letters greatly facilitate our review.  Please furnish your letter on EDGAR
under the form type label CORRESP.

 We urge all persons who are responsible for the accuracy and adequacy of the
disclosure in the filing to be certain that the filing includes all in formation required under
the Securities Exchange Act of 1934 and th at they have provided all information
investors require for an informed invest ment decision.  Since the company and its
management are in possession of all facts re lating to a company’s disclosure, they are
responsible for the accuracy and adequacy of the disclosures they have made.
  In connection with responding to our co mments, please provide, in your letter, a
statement from the company acknowledging that:
• the company is responsible for the adequacy  and accuracy of the disclosure in the
filing;
• staff comments or changes to disclosure  in response to staff comments do not
foreclose the Commission from taking any action with respect to the filing; and
• the company may not assert staff comme nts as a defense in any proceeding
initiated by the Commission or any person under the federal secu rities laws of the
United States.

In addition, please be advise d that the Division of Enfo rcement has access to all
information you provide to the staff of the Divi sion of Corporation Fi nance in our review
of your filing or in response to our comment on your filing.
Please contact Christine Allen, Staff A ccountant, at (202) 551- 3652 or Lisa
Vanjoske, Assistant Chief Accountant, at  (202) 551-3614 if you have any questions
regarding the processing of your response as well as any questions regarding comments
on the financial statements and related matte rs.  You may contact Michael Rosenthall,
Staff Attorney, at (202) 551-3674 or Jeffrey Ri edler, Associate Director, at (202) 551-
3715 with questions on any of the other commen ts.  In this regard, do not hesitate to
contact me, at (202) 551-3679.

Sincerely,

Jim B. Rosenberg Senior Assistant Chief Accountant